Gene signatures for cancer prognosis

ABSTRACT

Biomarkers and methods using the biomarkers for classifying cancer in a patient (e.g., predicting the risk of cancer-specific death or cancer recurrence) are provided.

CROSS-REFERENCE TO RELATED APPLICATION

This application is a continuation of International Application No.PCT/US2015/030617, filed May 13, 2015, which claims the benefit of U.S.Provisional Application No. 61/992,707, filed May 13, 2014 and U.S.Provisional Application No. 62/086,480, filed Dec. 2, 2014, the entirecontents of each of which are hereby incorporated by reference into thisapplication.

FIELD OF THE INVENTION

The disclosure generally relates to a molecular classification ofdisease and particularly to molecular markers for cancer prognosis andmethods of use thereof.

BACKGROUND OF THE INVENTION

Cancer is a major public health problem, accounting for roughly 25% ofall deaths in the United States. Though many treatments have beendevised for various cancers, these treatments often vary in severity ofside effects. It is useful for clinicians to know how aggressive apatient's cancer is in order to determine how aggressively to treat thecancer.

For example, most patients with early-stage asymptomatic prostate cancerare treated with radical prostatectomy or radiotherapy and optionallyadjuvant therapy (e.g., hormone or chemotherapy), all of which havesevere side effects. For many of these patients, however, thesetreatments and their associated side effects and costs are unnecessarybecause the cancer in these patients is not aggressive (i.e., growsslowly and is unlikely to cause mortality or significant morbidityduring the patient's lifetime). In other patients the cancer is virulent(i.e., more likely to recur) and aggressive treatment is necessary tosave the patient's life.

Some tools have been devised to help physicians in deciding whichpatients need aggressive treatment and which do not. In fact, severalclinical parameters are currently in use for this purpose in variousdifferent cancers. In prostate cancer, for example, such clinicalparameters include serum prostate-specific antigen (PSA), Gleason grade,pathologic stage, and surgical margins. In recent years clinicalparameters have been made more helpful through their incorporation intocontinuous multivariable postoperative nomograms that calculate apatient's probability of having cancer progression/recurrence. See,e.g., Kattan et al., J. CLIN. ONCOL. (1999) 17:1499-1507; Stephenson etal., J. CLIN. ONCOL. (2005) 23:7005-7012. Despite these advances,however, many patients are given improper cancer treatments and there isstill a serious need for novel and improved tools for predicting cancerrecurrence.

SUMMARY OF THE INVENTION

The present disclosure is based in part on the surprising discovery thatthe expression of those genes whose expression closely tracks the cellcycle (“cell-cycle genes” or “CCGs” as further defined below) isparticularly useful in classifying selected types of cancer anddetermining the prognosis of these cancers.

Accordingly, in a first aspect of the present disclosure, a method isprovided for determining gene expression in a tumor sample from apatient (e.g., one identified as having prostate cancer, lung cancer,bladder cancer or brain cancer). Generally, the method includes at leastthe following steps: (1) obtaining a tumor sample from a patient (e.g.,one identified as having prostate cancer, lung cancer, bladder cancer orbrain cancer); (2) determining the expression of a panel of genes insaid tumor sample including at least 4 cell-cycle genes; and (3)providing a test value by (a) weighting the determined expression ofeach of a plurality of test genes selected from said panel of genes witha predefined coefficient, and (b) combining the weighted expression toprovide said test value, wherein at least 50%, at least 75% or at least90% of said plurality of test genes are cell-cycle genes.

In some embodiments, the plurality of test genes includes at least 8cell-cycle genes, or at least 10, 15, 20, 25 or 30 cell-cycle genes. Insome embodiments, at least some proportion of the test genes (e.g., atleast 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 85%, 90%, 95%,or 99%) are cell-cycle genes. In some embodiments, all of the test genesare cell-cycle genes.

Also in some embodiments, the step of determining the expression of thepanel of genes in the tumor sample comprises measuring the amount ofmRNA in the tumor sample transcribed from each of from 4 to about 200cell-cycle genes; and measuring the amount of mRNA of one or morehousekeeping genes in the tumor sample.

In another aspect of the present disclosure, a method is provided fordetermining the prognosis of prostate cancer, lung cancer, bladdercancer or brain cancer, which comprises determining in a tumor samplefrom a patient diagnosed of prostate cancer, lung cancer, bladder canceror brain cancer, the expression of at least 6, 8 or 10 cell-cycle genes,wherein overexpression of said at least 6, 8 or 10 cell-cycle genesindicates a poor prognosis or an increased likelihood of recurrence ofcancer in the patient.

In one embodiment, the prognosis method comprises (1) determining in atumor sample from a patient diagnosed of prostate cancer, lung cancer,bladder cancer or brain cancer, the expression of a panel of genes insaid tumor sample including at least 4 or at least 8 cell-cycle genes;and (2) providing a test value by (a) weighting the determinedexpression of each of a plurality of test genes selected from the panelof genes with a predefined coefficient, and (b) combining the weightedexpression to provide the test value, wherein at least 50%, at least 75%or at least 85% of the plurality of test genes are cell-cycle genes, andwherein an increased level of overall expression of the plurality oftest genes indicates a poor prognosis, whereas if there is no increasein the overall expression of the test genes, it would indicate a goodprognosis or a low likelihood of recurrence of cancer in the patient.

In preferred embodiments, the prognosis method further includes a stepof comparing the test value provided in step (2) above to one or morereference values, and correlating the test value to a risk of cancerprogression or risk of cancer recurrence. In preferred embodiments, theprognosis method further includes a step of comparing the test valueprovided in step (2) above to one or more reference values, andcorrelating the test value to a likelihood (e.g., increased, decreased,specific percentage probability, etc.) of cancer progression, likelihoodof cancer recurrence, likelihood of cancer-specific death, or likelihoodof response to the particular treatment regimen. Optionally a test valuegreater than the reference value is correlated to an increasedlikelihood of response to treatment comprising chemotherapy. In someembodiments the test value is correlated to an increased likelihood ofresponse to treatment (e.g., treatment comprising chemotherapy) if thetest value exceeds the reference value by at least some amount (e.g., atleast 0.5, 0.75, 0.85, 0.90, 0.95, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 ormore fold or standard deviations). Optionally an increased likelihood ofpoor prognosis is indicated if the test value is greater than thereference value.

In yet another aspect, the present disclosure also provide a method oftreating cancer in a patient identified as having prostate cancer, lungcancer, bladder cancer or brain cancer, comprising: (1) determining in atumor sample from a patient diagnosed of prostate cancer, lung cancer,bladder cancer or brain cancer, the expression of a panel of genes inthe tumor sample including at least 4 or at least 8 cell-cycle genes;(2) providing a test value by (a) weighting the determined expression ofeach of a plurality of test genes selected from said panel of genes witha predefined coefficient, and (b) combining the weighted expression toprovide said test value, wherein at least 50% or 75% or 85% of theplurality of test genes are cell-cycle genes, wherein an increased levelof expression of the plurality of test genes indicates a poor prognosis,and an un-increased level of expression of the plurality of test genesindicates a good prognosis; and recommending, prescribing oradministering a treatment regimen or watchful waiting based on theprognosis provided in step (2).

The present disclosure further provides a diagnostic kit for prognosingcancer in a patient diagnosed of prostate cancer, lung cancer, bladdercancer or brain cancer, comprising, in a compartmentalized container, aplurality of oligonucleotides hybridizing to at least 8 test genes,wherein less than 10%, 30% or less than 40% of all of the at least 8test genes are non-cell-cycle genes; and one or more oligonucleotideshybridizing to at least one housekeeping gene. The oligonucleotides canbe hybridizing probes for hybridization with the test genes understringent conditions or primers suitable for PCR amplification of thetest genes. In one embodiment, the kit consists essentially of, in acompartmentalized container, a first plurality of PCR reaction mixturesfor PCR amplification of from 5 or 10 to about 300 test genes, whereinat least 50%, at least 60% or at least 80% of such test genes arecell-cycle genes, and wherein each reaction mixture comprises a PCRprimer pair for PCR amplifying one of the test genes; and a secondplurality of PCR reaction mixtures for PCR amplification of at least onehousekeeping gene. In some embodiments the kit comprises one or morecomputer software programs for calculating a test value derived from theexpression of the test genes (either the overall expression of all testgenes or of some subset) and for comparing this test value to somereference value (and optionally for assigning a risk level based on thiscomparison). In some embodiments such computer software is programmed toweight the test genes such that cell-cycle genes are weighted tocontribute at least 50%, at least 75% or at least 85% of the test value.In some embodiments such computer software is programmed to communicate(e.g., display) that the patient has an increased likelihood ofprogression, recurrence, cancer-specific death, or response to aparticular treatment regimen (e.g., comprising adjuvant radiation orchemotherapy) if the test value is greater than the reference value(e.g., by more than some predetermined amount). In some embodiments thecomputer software is programmed to communicate (e.g., display) the risklevel of progression, recurrence, cancer-specific death, or response toa particular treatment regimen assignable to the patient based on thetest value (e.g., based on comparison of the test value to a referencevalue).

The present disclosure also provides the use of (1) a plurality ofoligonucleotides hybridizing to at least 4 or at least 8 cell-cyclegenes; and (2) one or more oligonucleotides hybridizing to at least onehousekeeping gene, for the manufacture of a diagnostic product fordetermining the expression of the test genes in a tumor sample from apatient (e.g., one diagnosed with prostate cancer, lung cancer, bladdercancer or brain cancer) to predict the prognosis of cancer, wherein anincreased level of the overall expression of the test genes indicates apoor prognosis or an increased likelihood of recurrence of cancer in thepatient, whereas if there is no increase in the overall expression ofthe test genes, it would indicate a good prognosis or a low likelihoodof recurrence of cancer in the patient. In some embodiments, theoligonucleotides are PCR primers suitable for PCR amplification of thetest genes. In other embodiments, the oligonucleotides are probeshybridizing to the test genes under stringent conditions. In someembodiments, the plurality of oligonucleotides are probes forhybridization under stringent conditions to, or are suitable for PCRamplification of, from 4 to about 300 test genes, at least 50%, 70% or80% or 90% of the test genes being cell-cycle genes. In some otherembodiments, the plurality of oligonucleotides are hybridization probesfor, or are suitable for PCR amplification of, from 20 to about 300 testgenes, at least 30%, 40%, 50%, 70% or 80% or 90% of the test genes beingcell-cycle genes.

The present disclosure further provides a system for determining geneexpression in a tumor sample, comprising: (1) a sample analyzer fordetermining the expression levels of a panel of genes in a tumor sampleincluding at least 4 cell-cycle genes, wherein the sample analyzercontains the tumor sample (e.g., from a patient identified as havingprostate cancer, lung cancer, bladder cancer or brain cancer), mRNAexpressed from the panel of genes in the tumor sample, or cDNA moleculesfrom mRNA expressed from the panel of genes in the tumor sample; (2) afirst computer program for (a) receiving gene expression data on atleast 4 test genes selected from the panel of genes, (b) weighting thedetermined expression of each of the test genes with a predefinedcoefficient, and (c) combining the weighted expression to provide a testvalue, wherein at least 50%, at least at least 75% of at least 4 testgenes are cell-cycle genes; and optionally (3) a second computer programfor comparing the test value to one or more reference values eachassociated with a predetermined degree of risk of cancer recurrence orprogression of the prostate cancer, lung cancer, bladder cancer or braincancer. In some embodiments, the system further comprises a displaymodule displaying the comparison between the test value to the one ormore reference values, or displaying a result of the comparing step.

In some embodiments the disclosure provides a system for determining theprognosis of a patient having cancer, comprising: (1) a sample analyzerfor determining the expression levels of a panel of genes in a tumorsample including at least 4 cell-cycle genes, wherein the sampleanalyzer contains the tumor sample, mRNA molecules expressed from thepanel of genes and extracted from the sample, or cDNA molecules fromsaid mRNA molecules; (2) a first computer program for (a) receiving geneexpression data on at least 4 test genes selected from the panel ofgenes, (b) weighting the determined expression of each of the test geneswith a predefined coefficient, and (c) combining the weighted expressionto provide a test value, wherein the cell-cycle genes are weighted tocontribute at least 50%, at least 75% or at least 85% of the test value;and (3) a second computer program for comparing the test value to one ormore reference values each associated with a predetermined prognosis(e.g., a predetermined likelihood of recurrence, progression,cancer-specific death, or likelihood of response to a particulartreatment regimen). In some embodiments, the system further comprises adisplay module displaying the comparison between the test value and theone or more reference values, or displaying a result of the comparingstep.

In some embodiments, this disclosure provides methods of modifying thetreatment of an individual with prostate cancer

In some embodiments, the methods comprise:

-   -   (1) measuring, in a sample obtained from said individual, the        expression levels of a panel of genes comprising at least 3 test        genes selected from Panel F;    -   (2) providing a combined score by (a) weighting the determined        expression of each gene in said panel of genes with a predefined        coefficient (which may be 0), (b) weighting one or more clinical        parameters with a predefined coefficient (which may be 0),        and (c) combining the weighted expression of each gene in said        panel of genes and the weighted value of each clinical parameter        to provide said combined score, wherein said test genes are        weighted to contribute at least 25% to said combined score;    -   (3) comparing the combined score to a predetermined threshold;        and    -   (4) modifying the treatment of the individual to active        surveillance.

Unless otherwise defined, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this disclosure pertains. Although methods andmaterials similar or equivalent to those described herein can be used inthe practice or testing of the present disclosure, suitable methods andmaterials are described below. In case of conflict, the presentspecification, including definitions, will control. In addition, thematerials, methods, and examples are illustrative only and not intendedto be limiting.

Other features and advantages of the disclosure will be apparent fromthe following Detailed Description, and from the Claims.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is an illustration of the predictive power over nomogram for CCGpanels of different sizes.

FIG. 2 is an illustration of CCGs predicting time to recurrence.

FIG. 3 is an illustration of nomogram predicting time to recurrence.

FIG. 4 is an illustration of the non-overlapping recurrence predicted bynomogram and a CCG signature.

FIG. 5 is an illustration of time to recurrence for several patientpopulations defined by nomogram and/or CCG status.

FIG. 6 is an illustration of an example of a system useful in certainaspects and embodiments of the disclosure.

FIG. 7 is a flowchart illustrating an example of a computer-implementedmethod of the disclosure.

FIG. 8 a scatter plot comparing clinical parameters and CCG score aspredictors of recurrence from Example 5.

FIG. 9 illustrates, from Example 5, the CCG threshold derived fromanalysis of the training cohort to the validation data set, with the CCGsignature score effectively subdividing patients identified as low-riskusing clinical parameters into patients with very low recurrence ratesand a higher risk of recurrence.

FIG. 10 illustrates the predicted recurrence rate versus CCG score forpatients in the validation cohort of Example 5.

FIG. 11 illustrates the predicted recurrence rate versus CCG score forpatients in the validation cohort of Example 5.

FIG. 12 illustrates the distribution of clinical risk score in 443patients studied in Example 5. The dark vertical line represents thethreshold chosen by KM means to divide low- and high-risk patients andused throughout this study.

FIG. 13 illustrates the correlation between CCP score and survival inbrain cancer.

FIG. 14 illustrates the correlation between CCP score and survival inbladder cancer.

FIG. 15 illustrates the correlation between CCP score and survival inbreast cancer.

FIG. 16 illustrates the correlation between CCP score and survival inlung cancer.

FIG. 17 is an illustration of the predictive power over nomogram for CCGpanels of different sizes.

FIG. 18 shows the distribution of cases and controls by combined scorein Example 7.

FIG. 19 shows the distribution of observed p-values compared to theexpected (given no association) in Example 7.

FIG. 20 shows the RNA expression profiles underlying the significantp-values of six of the genes highlighted in Example 7.

FIG. 21 shows how KLK3 RNA expression levels predict case-control statusindependently of Gleason in Example 7.

FIG. 22 shows the RNA expression profiles underlying the significantp-values of six of the genes highlighted in Example 7.

FIG. 23 shows, graphically, exemplary prognoses (e.g., proportional riskof negative clinical outcome [biochemical recurrence or BCR])corresponding to various combined scores combining CCP score andclinical variables according to the equation: CombinedScore=0.38*(Clinical Variable(s))+0.57*(CCP Score).

FIG. 24 shows, graphically, exemplary prognoses (e.g., proportional riskof negative clinical outcome [prostate cancer-specific death or simply“death”]) corresponding to various combined scores combining CCP scoreand clinical variables according to the equation: CombinedScore=0.39*(Clinical Variable(s) (e.g., CAPRA))+0.57*(CCP Score).

FIG. 25 shows how the genes tested in Example 9 predicted outcome bothindependently and after adjusting for CCP score.

FIG. 26 shows graphically, CCP score versus KLK3 expression as describedin Example 9.

FIG. 27 shows prostate cancer survival against years after diagnosis byCCP score intervals as described in Example 9.

FIG. 28 shows prostate cancer survival against year after diagnosis byKLK3 intervals as described in Example 9.

FIG. 29 graphically shows the analysis of candidate androgen signalinggenes for prognostic utility as described in Example 10.

FIG. 30 graphically shows the distribution of combined scores in 505 menin a commercial testing population. A combined score threshold of 0.8 isindicated.

FIG. 31 shows a graph of Kaplan-Meier estimates of prostate cancer deathfor active surveillance qualified and non-active surveillance qualifiedindividuals with qualification based on a combined score threshold. Acombined score threshold of ≤0.6 for active surveillance dichotomizespatients into significantly different groups.

FIG. 32 shows a graph of Kaplan-Meier estimates of prostate cancer deathfor active surveillance qualified and non-active surveillance qualifiedindividuals, with qualification based on a combined score threshold. Acombined score threshold of ≤0.8 for active surveillance dichotomizespatients into significantly different groups.

FIG. 33 graphically shows the distribution of individuals in acommercial testing cohort who would or would not qualify for activesurveillance based on clinical parameters alone. A combined scorethreshold of 0.8 is indicated.

DETAILED DESCRIPTION OF THE INVENTION

I. Determining Cell-Cycle Gene Expression

The present disclosure is based in part on the discovery that geneswhose expression closely tracks the cell cycle (“cell-cycle genes” or“CCGs”) are particularly powerful genes for classifying selected cancersincluding prostate cancer, lung cancer, bladder cancer, brain cancer andbreast cancer, but not other types of cancer.

“Cell-cycle gene” and “CCG” herein refer to a gene whose expressionlevel closely tracks the progression of the cell through the cell-cycle.See, e.g., Whitfield et al., MOL. BIOL. CELL (2002) 13:1977-2000. Theterm “cell-cycle progression” or “CCP” will also be used in thisapplication and will generally be interchangeable with CCG (i.e., a CCPgene is a CCG; a CCP score is a CCG score). More specifically, CCGs showperiodic increases and decreases in expression that coincide withcertain phases of the cell cycle—e.g., STK15 and PLK show peakexpression at G2/M. Id. Often CCGs have clear, recognized cell-cyclerelated function—e.g., in DNA synthesis or repair, in chromosomecondensation, in cell-division, etc. However, some CCGs have expressionlevels that track the cell-cycle without having an obvious, direct rolein the cell-cycle—e.g., UBE2S encodes a ubiquitin-conjugating enzyme,yet its expression closely tracks the cell-cycle. Thus a CCG accordingto the present disclosure need not have a recognized role in thecell-cycle. Exemplary CCGs are listed in Tables 1, 2, 7-11, 13, 14 & A.A fuller discussion of CCGs can be found in International ApplicationNo. PCT/US2010/020397 (pub. no. WO/2010/080933) (see, e.g., Table 1 inWO/2010/080933), U.S. utility application Ser. No. 13/177,887 (pub. no.US20120041274), International Application No. PCT/US2011/043228 (pub.no. WO/2012/006447), and U.S. utility application Ser. No. 13/178,380(pub. no. US20120053253), the contents of which are hereby incorporatedby reference in their entirety.

Whether a particular gene is a CCG may be determined by any techniqueknown in the art, including those taught in Whitfield et al., MOL. BIOL.CELL (2002) 13:1977-2000; Whitfield et al., MOL. CELL. BIOL. (2000)20:4188-4198; WO/2010/080933 (¶ [0039]). All of the CCGs in Table 2below form a panel of CCGs (“Panel A”) useful in the disclosure. As willbe shown detail throughout this document, individual CCGs (e.g., CCGs inTable 2) and subsets of these genes can also be used in the disclosure.

TABLE 2 Entrez RefSeq Accession Gene Symbol GeneID ABI Assay ID Nos.APOBEC3B* 9582 Hs00358981_m1 NM_004900.3 ASF1B* 55723 Hs00216780_m1NM_018154.2 ASPM* 259266 Hs00411505_m1 NM_018136.4 ATAD2* 29028Hs00204205_m1 NM_014109.3 BIRC5* 332 Hs00153353_m1; NM_001012271.1;Hs03043576_m1 NM_001012270.1; NM_001168.2 BLM* 641 Hs00172060_m1NM_000057.2 BUB1 699 Hs00177821_m1 NM_004336.3 BUB1B* 701 Hs01084828_m1NM_001211.5 C12orf48* 55010 Hs00215575_m1 NM_017915.2 C18orf24* 220134Hs00536843_m1 NM_145060.3; NM_001039535.2 C1orf135* 79000 Hs00225211_m1NM_024037.1 C21orf45* 54069 Hs00219050_m1 NM_018944.2 CCDC99* 54908Hs00215019_m1 NM_017785.4 CCNA2* 890 Hs00153138_m1 NM_001237.3 CCNB1*891 Hs00259126_m1 NM_031966.2 CCNB2* 9133 Hs00270424_m1 NM_004701.2CCNE1* 898 Hs01026536_m1 NM_001238.1; NM_057182.1 CDC2* 983Hs00364293_m1 NM_033379.3; NM_001130829.1; NM_001786.3 CDC20* 991Hs03004916_g1 NM_001255.2 CDC45L* 8318 Hs00185895_m1 NM_003504.3 CDC6*990 Hs00154374_m1 NM_001254.3 CDCA3* 83461 Hs00229905_m1 NM_031299.4CDCA8* 55143 Hs00983655_m1 NM_018101.2 CDKN3* 1033 Hs00193192_m1NM_001130851.1; NM_005192.3 CDT1* 81620 Hs00368864_m1 NM_030928.3 CENPA1058 Hs00156455_m1 NM_001042426.1; NM_001809.3 CENPE* 1062 Hs00156507_m1NM_001813.2 CENPF* 1063 Hs00193201_m1 NM_016343.3 CENPI* 2491Hs00198791_m1 NM_006733.2 CENPM* 79019 Hs00608780_m1 NM_024053.3 CENPN*55839 Hs00218401_m1 NM_018455.4; NM_001100624.1; NM_001100625.1 CEP55*55165 Hs00216688_m1 NM_018131.4; NM_001127182.1 CHEK1* 1111Hs00967506_m1 NM_001114121.1; NM_001114122.1; NM_001274.4 CKAP2* 26586Hs00217068_m1 NM_018204.3; NM_001098525.1 CKS1B* 1163 Hs01029137_g1NM_001826.2 CKS2* 1164 Hs01048812_g1 NM_001827.1 CTPS* 1503Hs01041851_m1 NM_001905.2 CTSL2* 1515 Hs00952036_m1 NM_001333.2 DBF4*10926 Hs00272696_m1 NM_006716.3 DDX39* 10212 Hs00271794_m1 NM_005804.2DLGAP5/DLG7* 9787 Hs00207323_m1 NM_014750.3 DONSON* 29980 Hs00375083_m1NM_017613.2 DSN1* 79980 Hs00227760_m1 NM_024918.2 DTL* 51514Hs00978565_m1 NM_016448.2 E2F8* 79733 Hs00226635_m1 NM_024680.2 ECT2*1894 Hs00216455_m1 NM_018098.4 ESPL1* 9700 Hs00202246_m1 NM_012291.4EXO1* 9156 Hs00243513_m1 NM_130398.2; NM_003686.3; NM_006027.3 EZH2*2146 Hs00544830_m1 NM_152998.1; NM_004456.3 FANCI* 55215 Hs00289551_m1NM_018193.2; NM_001113378.1 FBXO5* 26271 Hs03070834_m1 NM_001142522.1;NM_012177.3 FOXM1* 2305 Hs01073586_m1 NM_202003.1; NM_202002.1;NM_021953.2 GINS1* 9837 Hs00221421_m1 NM_021067.3 GMPS* 8833Hs00269500_m1 NM_003875.2 GPSM2* 29899 Hs00203271_m1 NM_013296.4 GTSE1*51512 Hs00212681_m1 NM_016426.5 H2AFX* 3014 Hs00266783_s1 NM_002105.2HMMR* 3161 Hs00234864_m1 NM_001142556.1; NM_001142557.1; NM_012484.2;NM_012485.2 HN1* 51155 Hs00602957_m1 NM_001002033.1; NM_001002032.1;NM_016185.2 KIAA0101* 9768 Hs00207134_m1 NM_014736.4 KIF11* 3832Hs00189698_m1 NM_004523.3 KIF15* 56992 Hs00173349_m1 NM_020242.2 KIF18A*81930 Hs01015428_m1 NM_031217.3 KIF20A* 10112 Hs00993573_m1 NM_005733.2KIF20B/ 9585 Hs01027505_m1 NM_016195.2 MPHOSPH1* KIF23* 9493Hs00370852_m1 NM_138555.1; NM_004856.4 KIF2C* 11004 Hs00199232_m1NM_006845.3 KIF4A* 24137 Hs01020169_m1 NM_012310.3 KIFC1* 3833Hs00954801_m1 NM_002263.3 KPNA2 3838 Hs00818252_g1 NM_002266.2 LMNB2*84823 Hs00383326_m1 NM_032737.2 MAD2L1 4085 Hs01554513_g1 NM_002358.3MCAM* 4162 Hs00174838_m1 NM_006500.2 MCM10* 55388 Hs00960349_m1NM_018518.3; NM_182751.1 MCM2* 4171 Hs00170472_m1 NM_004526.2 MCM4* 4173Hs00381539_m1 NM_005914.2; NM_182746.1 MCM6* 4175 Hs00195504_m1NM_005915.4 MCM7* 4176 Hs01097212_m1 NM_005916.3; NM_182776.1 MELK 9833Hs00207681_m1 NM_014791.2 MKI67* 4288 Hs00606991_m1 NM_002417.3 MYBL2*4605 Hs00231158_m1 NM_002466.2 NCAPD2* 9918 Hs00274505_m1 NM_014865.3NCAPG* 64151 Hs00254617_m1 NM_022346.3 NCAPG2* 54892 Hs00375141_m1NM_017760.5 NCAPH* 23397 Hs01010752_m1 NM_015341.3 NDC80* 10403Hs00196101_m1 NM_006101.2 NEK2* 4751 Hs00601227_mH NM_002497.2 NUSAP1*51203 Hs01006195_m1 NM_018454.6; NM_001129897.1; NM_016359.3 OIP5* 11339Hs00299079_m1 NM_007280.1 ORC6L* 23594 Hs00204876_m1 NM_014321.2 PAICS*10606 Hs00272390_m1 NM_001079524.1; NM_001079525.1; NM_006452.3 PBK*55872 Hs00218544_m1 NM_018492.2 PCNA* 5111 Hs00427214_g1 NM_182649.1;NM_002592.2 PDSS1* 23590 Hs00372008_m1 NM_014317.3 PLK1* 5347Hs00153444_m1 NM_005030.3 PLK4* 10733 Hs00179514_m1 NM_014264.3 POLE2*5427 Hs00160277_m1 NM_002692.2 PRC1* 9055 Hs00187740_m1 NM_199413.1;NM_199414.1; NM_003981.2 PSMA7* 5688 Hs00895424_m1 NM_002792.2 PSRC1*84722 Hs00364137_m1 NM_032636.6; NM_001005290.2; NM_001032290.1;NM_001032291.1 PTTG1* 9232 Hs00851754_u1 NM_004219.2 RACGAP1* 29127Hs00374747_m1 NM_013277.3 RAD51* 5888 Hs00153418_m1 NM_133487.2;NM_002875.3 RAD51AP1* 10635 Hs01548891_m1 NM_001130862.1; NM_006479.4RAD54B* 25788 Hs00610716_m1 NM_012415.2 RAD54L* 8438 Hs00269177_m1NM_001142548.1; NM_003579.3 RFC2* 5982 Hs00945948_m1 NM_181471.1;NM_002914.3 RFC4* 5984 Hs00427469_m1 NM_181573.2; NM_002916.3 RFC5* 5985Hs00738859_m1 NM_181578.2; NM_001130112.1; NM_001130113.1; NM_007370.4RNASEH2A* 10535 Hs00197370_m1 NM_006397.2 RRM2* 6241 Hs00357247_g1NM_001034.2 SHCBP1* 79801 Hs00226915_m1 NM_024745.4 SMC2* 10592Hs00197593_m1 NM_001042550.1; NM_001042551.1; NM_006444.2 SPAG5* 10615Hs00197708_m1 NM_006461.3 SPC25* 57405 Hs00221100_m1 NM_020675.3 STIL*6491 Hs00161700_m1 NM_001048166.1; NM_003035.2 STMN1* 3925Hs00606370_m1; NM_005563.3; Hs01033129_m1 NM_203399.1 TACC3* 10460Hs00170751_m1 NM_006342.1 TIMELESS* 8914 Hs01086966_m1 NM_003920.2 TK1*7083 Hs01062125_m1 NM_003258.4 TOP2A* 7153 Hs00172214_m1 NM_001067.2TPX2* 22974 Hs00201616_m1 NM_012112.4 TRIP13* 9319 Hs01020073_m1NM_004237.2 TTK* 7272 Hs00177412_m1 NM_003318.3 TUBA1C* 84790Hs00733770_m1 NM_032704.3 TYMS* 7298 Hs00426591_m1 NM_001071.2 UBE2C11065 Hs00964100_g1 NM_181799.1; NM_181800.1; NM_181801.1; NM_181802.1;NM_181803.1; NM_007019.2 UBE2S 27338 Hs00819350_m1 NM_014501.2 VRK1*7443 Hs00177470_m1 NM_003384.2 ZWILCH* 55055 Hs01555249_m1 NM_017975.3;NR_003105.1 ZWINT* 11130 Hs00199952_m1 NM_032997.2; NM_001005413.1;NM_007057.3 *124-gene subset of CCGs useful in the disclosure (“PanelB”). ABI Assay ID means the catalogue ID number for the gene expressionassay commercially available from Applied Biosystems Inc. (Foster City,CA) for the particular gene.

Accordingly, in a first aspect of the present disclosure, a method isprovided for determining gene expression in a tumor sample from apatient (e.g., one identified as having prostate cancer, lung cancer,bladder cancer or brain cancer). Generally, the method includes at leastthe following steps: (1) obtaining a tumor sample from a patient (e.g.,one identified as having prostate cancer, lung cancer, bladder cancer orbrain cancer); (2) determining the expression of a panel of genes in thetumor sample including at least 2, 4, 6, 8 or 10 cell-cycle genes; and(3) providing a test value by (a) weighting the determined expression ofeach of a plurality of test genes selected from said panel of genes witha predefined coefficient, and (b) combining the weighted expression toprovide said test value, wherein at least 20%, 50%, at least 75% or atleast 90% of said plurality of test genes are cell-cycle genes. In someembodiments the test genes are weighted such that the cell-cycle genesare weighted to contribute at least 50%, at least 55%, at least 60%, atleast 65%, at least 75%, at least 80%, at least 85%, at least 90%, atleast 95%, at least 99% or 100% of the test value. In some embodiments20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 75%, 80%, 85%, 90%,95%, or at least 99% or 100% of the plurality of test genes arecell-cycle genes.

Gene expression can be determined either at the RNA level (i.e., mRNA ornoncoding RNA (ncRNA)) (e.g., miRNA, tRNA, rRNA, snoRNA, siRNA andpiRNA) or at the protein level. Measuring gene expression at the mRNAlevel includes measuring levels of cDNA corresponding to mRNA. Levels ofproteins in a tumor sample can be determined by any known techniques inthe art, e.g., HPLC, mass spectrometry, or using antibodies specific toselected proteins (e.g., IHC, ELISA, etc.).

In preferred embodiment, the amount of RNA transcribed from the panel ofgenes including test genes is measured in the tumor sample. In addition,the amount of RNA of one or more housekeeping genes in the tumor sampleis also measured, and used to normalize or calibrate the expression ofthe test genes. The terms “normalizing genes” and “housekeeping genes”are defined herein below.

In any embodiment of the disclosure involving a “plurality of testgenes,” the plurality of test genes may include at least 2, 3 or 4cell-cycle genes, which constitute at least 50%, 75% or 80% of theplurality of test genes, and preferably 100% of the plurality of testgenes. In some embodiments, the plurality of test genes includes atleast 5, 6, 7, or at least 8 cell-cycle genes, which constitute at least20%, 25%, 30%, 40%, 50%, 60%, 70%, 75%, 80% or 90% of the plurality oftest genes, and preferably 100% of the plurality of test genes. As willbe clear from the context of this document, a panel of genes is aplurality of genes. Typically these genes are assayed together in one ormore samples from a patient.

In some other embodiments, the plurality of test genes includes at least8, 10, 12, 15, 20, 25 or 30 cell-cycle genes, which constitute at least20%, 25%, 30%, 40%, 50%, 60%, 70%, 75%, 80% or 90% of the plurality oftest genes, and preferably 100% of the plurality of test genes.

As will be apparent to a skilled artisan apprised of the presentdisclosure and the disclosure herein, “tumor sample” means anybiological sample containing one or more tumor cells, or one or moretumor derived RNA or protein, and obtained from a cancer patient. Forexample, a tissue sample obtained from a tumor tissue of a cancerpatient is a useful tumor sample in the present disclosure. The tissuesample can be an FFPE sample, or fresh frozen sample, and preferablycontain largely tumor cells. A single malignant cell from a cancerpatient's tumor is also a useful tumor sample. Such a malignant cell canbe obtained directly from the patient's tumor, or purified from thepatient's bodily fluid (e.g., blood, urine). Thus, a bodily fluid suchas blood, urine, sputum and saliva containing one or tumor cells, ortumor-derived RNA or proteins, can also be useful as a tumor sample forpurposes of practicing the present disclosure.

Those skilled in the art are familiar with various techniques fordetermining the status of a gene or protein in a tissue or cell sampleincluding, but not limited to, microarray analysis (e.g., for assayingmRNA or microRNA expression, copy number, etc.), quantitative real-timePCR™ (“qRT-PCR™”, e.g., TaqMan™), immunoanalysis (e.g., ELISA,immunohistochemistry), etc. The activity level of a polypeptide encodedby a gene may be used in much the same way as the expression level ofthe gene or polypeptide. Often higher activity levels indicate higherexpression levels and while lower activity levels indicate lowerexpression levels. Thus, in some embodiments, the disclosure providesany of the methods discussed above, wherein the activity level of apolypeptide encoded by the CCG is determined rather than or in additionto the expression level of the CCG. Those skilled in the art arefamiliar with techniques for measuring the activity of various suchproteins, including those encoded by the genes listed in Tables 1 & 2.The methods of the disclosure may be practiced independent of theparticular technique used.

In preferred embodiments, the expression of one or more normalizing(often called “housekeeping”) genes is also obtained for use innormalizing the expression of test genes. As used herein, “normalizinggenes” referred to the genes whose expression is used to calibrate ornormalize the measured expression of the gene of interest (e.g., testgenes). Importantly, the expression of normalizing genes should beindependent of cancer outcome/prognosis, and the expression of thenormalizing genes is very similar among all the tumor samples. Thenormalization ensures accurate comparison of expression of a test genebetween different samples. For this purpose, housekeeping genes known inthe art can be used. Housekeeping genes are well known in the art, withexamples including, but are not limited to, GUSB (glucuronidase, beta),HMBS (hydroxymethylbilane synthase), SDHA (succinate dehydrogenasecomplex, subunit A, flavoprotein), UBC (ubiquitin C) and YWHAZ (tyrosine3-monooxygenase/tryptophan 5-monooxygenase activation protein, zetapolypeptide). One or more housekeeping genes can be used. Preferably, atleast 2, 5, 10 or 15 housekeeping genes are used to provide a combinednormalizing gene set. The amount of gene expression of such normalizinggenes can be averaged, combined together by straight additions or by adefined algorithm. Some examples of particularly useful housekeepergenes for use in the methods and compositions of the disclosure includethose listed in Table 3 below.

TABLE 3 Gene Entrez Applied Biosystems Symbol GeneID Assay ID RefSeqAccession Nos. CLTC* 1213 Hs00191535_m1 NM_004859.3 GUSB 2990Hs99999908_m1 NM_000181.2 HMBS 3145 Hs00609297_m1 NM_000190.3 MMADHC*27249 Hs00739517_g1 NM_015702.2 MRFAP1* 93621 Hs00738144_g1 NM_033296.1PPP2CA* 5515 Hs00427259_m1 NM_002715.2 PSMA1* 5682 Hs00267631_m1 PSMC1*5700 Hs02386942_g1 NM_002802.2 RPL13A* 23521 Hs03043885_g1 NM_012423.2RPL37* 6167 Hs02340038_g1 NM_000997.4 RPL38* 6169 Hs00605263_g1NM_000999.3 RPL4* 6124 Hs03044647_g1 NM_000968.2 RPL8* 6132Hs00361285_g1 NM_033301.1; NM_000973.3 RPS29* 6235 Hs03004310_g1NM_001030001.1; NM_001032.3 SDHA 6389 Hs00188166_m1 NM_004168.2 SLC25A3*6515 Hs00358082_m1 NM_213611.1; NM_002635.2; NM_005888.2 TXNL1* 9352Hs00355488_m1 NR_024546.1; NM_004786.2 UBA52* 7311 Hs03004332_g1NM_001033930.1; NM_003333.3 UBC 7316 Hs00824723_m1 NM_021009.4 YWHAZ7534 Hs00237047_m1 NM_003406.3 *Subset of housekeeping genes used in,e.g., Example 5.

In the case of measuring RNA levels for the genes, one convenient andsensitive approach is real-time quantitative PCR™ (qPCR) assay,following a reverse transcription reaction. Typically, a cycle threshold(C_(t)) is determined for each test gene and each normalizing gene,i.e., the number of cycles at which the fluorescence from a qPCRreaction above background is detectable.

The overall expression of the one or more normalizing genes can berepresented by a “normalizing value” which can be generated by combiningthe expression of all normalizing genes, either weighted equally(straight addition or averaging) or by different predefinedcoefficients. For example, in a simplest manner, the normalizing valueC_(tH) can be the cycle threshold (C_(t)) of one single normalizinggene, or an average of the C_(t) values of 2 or more, preferably 10 ormore, or 15 or more normalizing genes, in which case, the predefinedcoefficient is 1/N, where N is the total number of normalizing genesused. Thus, C_(tH)=(C_(tH1)+C_(tH2)+−C_(tHn))/N. As will be apparent toskilled artisans, depending on the normalizing genes used, and theweight desired to be given to each normalizing gene, any coefficients(from 0/N to N/N) can be given to the normalizing genes in weighting theexpression of such normalizing genes. That is,C_(tH)=xC_(tH1)+yC_(tH2)+−zC_(tHn), wherein x+y+ . . . +z=1.

As discussed above, the methods of the disclosure generally involvedetermining the level of expression of a panel of CCGs. With modernhigh-throughput techniques, it is often possible to determine theexpression level of tens, hundreds or thousands of genes. Indeed, it ispossible to determine the level of expression of the entiretranscriptome (i.e., each transcribed sequence in the genome). Once sucha global assay has been performed, one may then informatically analyzeone or more subsets of transcripts (i.e., panels or, as often usedherein, pluralities of test genes). After measuring the expression ofhundreds or thousands of transcripts in a sample, for example, one mayanalyze (e.g., informatically) the expression of a panel or plurality oftest genes comprising primarily CCGs according to the present disclosureby combining the expression level values of the individual test genes toobtain a test value.

As will be apparent to a skilled artisan, the test value provided in thepresent disclosure represents the overall expression level of theplurality of test genes composed substantially of cell-cycle genes. Inone embodiment, to provide a test value in the methods of thedisclosure, the normalized expression for a test gene can be obtained bynormalizing the measured C_(t) for the test gene against the C_(tH),i.e., ΔC_(t1)=(C_(t1)−C_(tH)). Thus, the test value representing theoverall expression of the plurality of test genes can be provided bycombining the normalized expression of all test genes, either bystraight addition or averaging (i.e., weighted equally) or by adifferent predefined coefficient. For example, the simplest approach isaveraging the normalized expression of all test genes: testvalue=(ΔC_(t1)+ΔC_(t2)+ . . . +ΔC_(tn))/n. As will be apparent toskilled artisans, depending on the test genes used, different weight canalso be given to different test genes in the present disclosure. In eachcase where this document discloses using the expression of a pluralityof genes (e.g., “determining [in a tumor sample from the patient] theexpression of a plurality of test genes” or “correlating increasedexpression of said plurality of test genes to an increased likelihood ofrecurrence”), this includes in some embodiments using a test valuerepresenting, corresponding to or derived or calculated from the overallexpression of this plurality of genes (e.g., “determining [in a tumorsample from the patient] a test value representing the expression of aplurality of test genes” or “correlating an increased test value [or atest value above some reference value] (optionally representing theexpression of said plurality of test genes) to an increased likelihoodof response”).

It has been determined that, once the CCP phenomenon reported herein isappreciated, the choice of individual CCGs for a test panel can often besomewhat arbitrary. In other words, many CCGs have been found to be verygood surrogates for each other. Thus any CCG (or panel of CCGs) can beused in the various embodiments of the disclosure. In other embodimentsof the disclosure, optimized CCGs are used. One way of assessing whetherparticular CCGs will serve well in the methods and compositions of thedisclosure is by assessing their correlation with the mean expression ofCCGs (e.g., all known CCGs, a specific set of CCGs, etc.). Those CCGsthat correlate particularly well with the mean are expected to performwell in assays of the disclosure, e.g., because these will reduce noisein the assay.

126 CCGs and 47 housekeeping genes had their expression compared to theCCG and housekeeping mean in order to determine preferred genes for usein some embodiments of the disclosure. Rankings of select CCGs accordingto their correlation with the mean CCG expression as well as theirranking according to predictive value are given in Tables 9-11, & 13-14.

Thus, in some embodiments of each of the various aspects of thedisclosure the plurality of test genes comprises the top 2, 3, 4, 5, 6,7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 35, 40 or more CCGs listedin Tables 9-11, & 13-14. In some embodiments the plurality of test genescomprises at least some number of CCGs (e.g., at least 3, 4, 5, 6, 7, 8,9, 10, 15, 20, 25, 30, 35, 40, 45, 50 or more CCGs) and this pluralityof CCGs comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, or 20 ofthe following genes: ASPM, BIRC5, BUB1B, CCNB2, CDC2, CDC20, CDCA8,CDKN3, CENPF, DLGAP5, FOXM1, KIAA0101, KIF11, KIF2C, KIF4A, MCM10,NUSAP1, PRC1, RACGAP1, and TPX2. In some embodiments the plurality oftest genes comprises at least some number of CCGs (e.g., at least 3, 4,5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50 or more CCGs) and thisplurality of CCGs comprises any two, three, four, five, six, seven,eight, nine, or ten or all of gene numbers 1 & 2, 1 to 3, 1 to 4, 1 to5, 1 to 6, 1 to 7, 1 to 8, 1 to 9, or 1 to 10 of any of Tables 9-11, &13-14. In some embodiments the plurality of test genes comprises atleast some number of CCGs (e.g., at least 3, 4, 5, 6, 7, 8, 9, 10, 15,20, 25, 30, 35, 40, 45, 50 or more CCGs) and this plurality of CCGscomprises any one, two, three, four, five, six, seven, eight, or nine orall of gene numbers 2 & 3, 2 to 4, 2 to 5, 2 to 6, 2 to 7, 2 to 8, 2 to9, or 2 to 10 of any of Tables 9-11, & 13-14. In some embodiments theplurality of test genes comprises at least some number of CCGs (e.g., atleast 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50 or moreCCGs) and this plurality of CCGs comprises any one, two, three, four,five, six, seven, or eight or all of gene numbers 3 & 4, 3 to 5, 3 to 6,3 to 7, 3 to 8, 3 to 9, or 3 to 10 of any of Tables 9-11, & 13-14. Insome embodiments the plurality of test genes comprises at least somenumber of CCGs (e.g., at least 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30,35, 40, 45, 50 or more CCGs) and this plurality of CCGs comprises anyone, two, three, four, five, six, or seven or all of gene numbers 4 & 5,4 to 6, 4 to 7, 4 to 8, 4 to 9, or 4 to 10 of any of Tables 9-11, &13-14. In some embodiments the plurality of test genes comprises atleast some number of CCGs (e.g., at least 3, 4, 5, 6, 7, 8, 9, 10, 15,20, 25, 30, 35, 40, 45, 50 or more CCGs) and this plurality of CCGscomprises any one, two, three, four, five, six, seven, eight, nine, 10,11, 12, 13, 14, or 15 or all of gene numbers 1 & 2, 1 to 3, 1 to 4, 1 to5, 1 to 6, 1 to 7, 1 to 8, 1 to 9, 1 to 10, 1 to 11, 1 to 12, 1 to 13, 1to 14, or 1 to 15 of any of Tables 9-11, & 13-14.

II. Cancer Prognosis

It has been surprisingly discovered that in selected cancers such asprostate cancer, lung cancer, bladder cancer and brain cancer, but notother cancers including certain colon cancer, the expression ofcell-cycle genes in tumor cells can accurately predict the degree ofaggression of the cancer and risk of recurrence after treatment (e.g.,surgical removal of cancer tissue, chemotherapy and radiation therapy,etc.). Thus, the above-described method of determining cell-cycle geneexpression can be applied in the prognosis and treatment of suchcancers.

Generally, a method is provided for prognosing cancer selected fromprostate cancer, lung cancer, bladder cancer or brain cancer, whichcomprises determining in a tumor sample from a patient diagnosed ofprostate cancer, lung cancer, bladder cancer or brain cancer, theexpression of at least 2, 4, 5, 6, 7 or at least 8, 9, 10 or 12cell-cycle genes, wherein high expression (or increased expression oroverexpression) of the at least 4 cell-cycle genes indicates a poorprognosis or an increased likelihood of recurrence of cancer in thepatient. The expression can be determined in accordance with the methoddescribed above. In some embodiments, the method comprises at least oneof the following steps: (a) correlating high expression (or increasedexpression or overexpression) of the cell-cycle genes to a poorprognosis or an increased likelihood of recurrence of cancer in thepatient; (b) concluding that the patient has a poor prognosis or anincreased likelihood of recurrence of cancer based at least in part onhigh expression (or increased expression or overexpression) of thecell-cycle genes; or (c) communicating that the patient has a poorprognosis or an increased likelihood of recurrence of cancer based atleast in part on high expression (or increased expression oroverexpression) of the cell-cycle genes.

In each embodiment described in this document involving correlating aparticular assay or analysis output (e.g., high CCP expression, testvalue incorporating CCP expression greater than some reference value,etc.) to some likelihood (e.g., increased, not increased, decreased,etc.) of some clinical event or outcome (e.g., recurrence, progression,cancer-specific death, etc.), such correlating may comprise assigning arisk or likelihood of the clinical event or outcome occurring based atleast in part on the particular assay or analysis output. In someembodiments, such risk is a percentage probability of the event oroutcome occurring. In some embodiments, the patient is assigned to arisk group (e.g., low risk, intermediate risk, high risk, etc.). In someembodiments “low risk” is any percentage probability below 5%, 10%, 15%,20%, 25%, 30%, 35%, 40%, 45%, or 50%. In some embodiments “intermediaterisk” is any percentage probability above 5%, 10%, 15%, 20%, 25%, 30%,35%, 40%, 45%, or 50% and below 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%,55%, 60%, 65%, 70%, or 75%. In some embodiments “high risk” is anypercentage probability above 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%,65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99%.

As used herein, “communicating” a particular piece of information meansto make such information known to another person or transfer suchinformation to a thing (e.g., a computer). In some methods of thedisclosure, a patient's prognosis or risk of recurrence is communicated.In some embodiments, the information used to arrive at such a prognosisor risk prediction (e.g., expression levels of a panel of biomarkerscomprising a plurality of CCGs, clinical or pathologic factors, etc.) iscommunicated. This communication may be auditory (e.g., verbal), visual(e.g., written), electronic (e.g., data transferred from one computersystem to another), etc. In some embodiments, communicating a cancerclassification comprises generating a report that communicates thecancer classification. In some embodiments the report is a paper report,an auditory report, or an electronic record. In some embodiments thereport is displayed and/or stored on a computing device (e.g., handhelddevice, desktop computer, smart device, website, etc.). In someembodiments the cancer classification is communicated to a physician(e.g., a report communicating the classification is provided to thephysician). In some embodiments the cancer classification iscommunicated to a patient (e.g., a report communicating theclassification is provided to the patient). Communicating a cancerclassification can also be accomplished by transferring information(e.g., data) embodying the classification to a server computer andallowing an intermediary or end-user to access such information (e.g.,by viewing the information as displayed from the server, by downloadingthe information in the form of one or more files transferred from theserver to the intermediary or end-user's device, etc.).

Wherever an embodiment of the disclosure comprises concluding some fact(e.g., a patient's prognosis or a patient's likelihood of recurrence),this may include a computer program concluding such fact, typicallyafter performing an algorithm that applies information on CCG status,PTEN status, KLK3 status, PCA3 status and/or clinical variables in apatient sample (e.g., as shown in FIG. 7).

In some embodiments, the prognosis method includes (1) obtaining a tumorsample from a patient identified as having prostate cancer, lung cancer,bladder cancer or brain cancer; (2) determining the expression of apanel of genes in the tumor sample including at least 2, 4, 6, 8 or 10cell-cycle genes; and (3) providing a test value by (a) weighting thedetermined expression of each of a plurality of test genes selected fromthe panel of genes with a predefined coefficient, and (b) combining theweighted expression to provide said test value, wherein at least 20%,50%, at least 75% or at least 90% of said plurality of test genes arecell-cycle genes, and wherein high expression (or increased expressionor overexpression) of the plurality of test genes indicates a poorprognosis or an increased likelihood of cancer recurrence. In someembodiments, the method comprises at least one of the following steps:(a) correlating high expression (or increased expression oroverexpression) of the plurality of test genes to a poor prognosis or anincreased likelihood of recurrence of cancer in the patient; (b)concluding that the patient has a poor prognosis or an increasedlikelihood of recurrence of cancer based at least in part on highexpression (or increased expression or overexpression) of the pluralityof test genes; or (c) communicating that the patient has a poorprognosis or an increased likelihood of recurrence of cancer based atleast in part on high expression (or increased expression oroverexpression) of the plurality of test genes.

In some embodiments, the expression levels measured in a sample are usedto derive or calculate a value or score. This value may be derivedsolely from these expression levels (e.g., a CCG score) or optionallyderived from a combination of the expression value/score with othercomponents (e.g., year of RP, surgical margins, extracapsular extension,seminal vesicle invasion, lymph node involvement, primary Gleason score,secondary Gleason score, or preoperative PSA level, etc.) to give a morecomprehensive value/score. Thus, in every case where an embodiment ofthe disclosure described herein involves determining the status of abiomarker (e.g., RNA expression levels of a CCG, PTEN, or KLK3), relatedembodiments involve deriving or calculating a value or score from themeasured status (e.g., expression score).

In some such embodiments, multiple scores (e.g., CCG, Gleason, PSA,PTEN, KLK3, PCA3) can be combined into a more comprehensive score.Single component (e.g., CCG) or combined test scores for a particularpatient can be compared to single component or combined scores forreference populations as described below, with differences between testand reference scores being correlated to or indicative of some clinicalfeature. Thus, in some embodiments the disclosure provides a method ofdetermining a cancer patient's prognosis comprising (1) obtaining themeasured expression levels of a plurality of genes comprising aplurality of CCGs in a sample from the patient, (2) calculating a testvalue from these measured expression levels, (3) comparing said testvalue to a reference value calculated from measured expression levels ofthe plurality of genes in a reference population of patients, and (4)(a)correlating a test value greater than the reference value to a poorprognosis or (4)(b) correlating a test value equal to or less than thereference value to a good prognosis.

In some such embodiments the test value is calculated by averaging themeasured expression of the plurality of genes (as discussed below). Insome embodiments the test value is calculated by weighting each of theplurality of genes in a particular way.

In some embodiments the plurality of CCGs are weighted such that theycontribute at least some proportion of the test value (e.g., 10%, 20%,30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 99%, 100%). In some embodimentseach of the plurality of genes is weighted such that not all are givenequal weight (e.g., KLK3 or PCA3 weighted to contribute more to the testvalue than one, some or all CCGs).

In some embodiments CCP expression is weighted and combined with otherfactors into a combined score (similar to the test value discussedabove). In some embodiments such a combined score is calculated byadding the CCP score and the other factor(s) linearly according to thefollowing formula:Combined score=A*(CCP score)+B*(One or more other factors)  (1)It will be appreciated that this disclosure encompasses other means ofcombination (e.g., multiplication, logarithms, exponents, etc.). In someembodiments the other factors are expression of other genes, physicalcharacteristics of the patient (e.g., height, weight, etc.), clinicalcharacteristics of the patient (e.g., clinical variables as discussedbelow), etc. In some embodiments one or more clinical variables can becombined into a clinical score, which can then be combined with the CCPscore to yield a Combined Score of the disclosure.

Thus, in some embodiments the disclosure provides an method ofdetermining a cancer patient's prognosis comprising: (1) obtaining themeasured expression levels of a plurality of genes comprising aplurality of CCGs in a sample from the patient; (2) obtaining a scorefor the patient comprising one or more of year of RP, surgical margins,extracapsular extension, seminal vesicle invasion, lymph nodeinvolvement, primary Gleason score, secondary Gleason score, orpreoperative PSA level; (3) deriving a combined test value from themeasured levels obtained in (1) and the score obtained in (2); (4)comparing the combined test value to a combined reference value derivedfrom measured expression levels of the plurality of genes and a scorecomprising one or more of year of RP, surgical margins, extracapsularextension, seminal vesicle invasion, lymph node involvement, primaryGleason score, secondary Gleason score, or preoperative PSA level in areference population of patients; and (5)(a) correlating a combined testvalue greater than the combined reference value to a poor prognosis or(5)(b) correlating a combined test value equal to or less than thecombined reference value to a good prognosis.

In some embodiments the combined score includes CCP score, PSA, andGleason score. CCP can be a continuous numeric variable. PSAconcentrations (e.g., ng/dL), adding 1 to avoid zero values, can betransformed by the natural logarithm. Gleason scores can be a continuousnumeric variable or can be categorized, e.g., as <7 (reference level),7, and >7. In some embodiments Gleason scores can be input as theirnumerical value (rather than being grouped). In some embodiments aGleason score of 7 can be further delineated by (3+4) versus (4+3).

In some embodiments the combined score is calculated according to thefollowing formula:Combined score=A*(CCP score)+B*(ln(1+[PSA]))+{C(if Gleason=7) or D (ifGleason>7)}  (2)In some embodiments clinical variables (e.g., PSA, Gleason, etc.) can becombined into a clinical score (e.g., nomogram score), which can then becombined with the CCP score to yield a Combined Score according to thefollowing formula:Combined Score=A*(CCP score)+B*(clinical score)  (3)In some embodiments the clinical score is the CAPRA score or theKattan-Stephenson nomogram score. CAPRA score may be calculated asdiscussed herein (see especially Example 8 below). In some embodimentsthe clinical score is not a combination of clinical variables butinstead a score representing one variable (e.g., Gleason score).

The Combined Score with CCP and other components weighted as discussedherein encompasses, mutatis mutandis, any modified or scaled versionthereof. For instance, the elements can be multiplied or divided by afactor (e.g., constant or new variable) and/or have a factor (e.g.,constant or new variable) added or subtracted. As an example, a CombinedScore according to formula (3)Combined Score=A*(CCP score)+B*(clinical score)  (3)encompasses a version thereof scales by the factors C and D according tothe following formula (3A)Combined Score=C*(A*(CCP score)+B*(clinical score))+D  (3A)

In some embodiments, any of the formulae discussed herein is used in themethods, systems, etc. of the disclosure to determine prognosis based ona patient's radical prostatectomy sample. In some embodiments, any ofthe formulae discussed herein is used in the methods, systems, etc. ofthe disclosure to determine prognosis based on a patient's prostatebiopsy sample. In some embodiments CCP score is the unweighted mean ofC_(T) values for expression of the CCP genes being analyzed, optionallynormalized by the unweighted mean of the HK genes so that higher valuesindicate higher expression (in some embodiments one unit is equivalentto a two-fold change in expression). In some embodiments the CCP scoreranges from −8 to 8 or from −1.6 to 3.7.

In some embodiments A=0.95, B=0.61, C=0.90 (where applicable), & D=1.00(where applicable); A=0.57 & B=0.39; or A=0.58 & B=0.41. In someembodiments, A, B, C, and/or D is within rounding of these values (e.g.,A is between 0.945 and 0.954, etc.). In some cases a formula may nothave all of the specified coefficients (and thus not incorporate thecorresponding variable(s)). For example, the embodiment mentionedimmediately previously may be applied to formula (3) where A in formula(3) is 0.95 and B in formula (3) is 0.61. C and D would not beapplicable as these coefficients and their corresponding variables arenot found in formula (3) (though the clinical variables may beincorporated into the clinical score found in formula (3)). In someembodiments A is between 0.9 and 1, 0.9 and 0.99, 0.9 and 0.95, 0.85 and0.95, 0.86 and 0.94, 0.87 and 0.93, 0.88 and 0.92, 0.89 and 0.91, 0.85and 0.9, 0.8 and 0.95, 0.8 and 0.9, 0.8 and 0.85, 0.75 and 0.99, 0.75and 0.95, 0.75 and 0.9, 0.75 and 0.85, or between 0.75 and 0.8. In someembodiments B is between 0.40 and 1, 0.45 and 0.99, 0.45 and 0.95, 0.55and 0.8, 0.55 and 0.7, 0.55 and 0.65, 0.59 and 0.63, or between 0.6 and0.62. In some embodiments C is, where applicable, between 0.9 and 1, 0.9and 0.99, 0.9 and 0.95, 0.85 and 0.95, 0.86 and 0.94, 0.87 and 0.93,0.88 and 0.92, 0.89 and 0.91, 0.85 and 0.9, 0.8 and 0.95, 0.8 and 0.9,0.8 and 0.85, 0.75 and 0.99, 0.75 and 0.95, 0.75 and 0.9, 0.75 and 0.85,or between 0.75 and 0.8. In some embodiments D is, where applicable,between 0.9 and 1, 0.9 and 0.99, 0.9 and 0.95, 0.85 and 0.95, 0.86 and0.94, 0.87 and 0.93, 0.88 and 0.92, 0.89 and 0.91, 0.85 and 0.9, 0.8 and0.95, 0.8 and 0.9, 0.8 and 0.85, 0.75 and 0.99, 0.75 and 0.95, 0.75 and0.9, 0.75 and 0.85, or between 0.75 and 0.8.

In some embodiments A is between 0.1 and 0.2, 0.3, 0.4, 0.5, 0.6, 0.7,0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, or 20; or between 0.2 and 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1,1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or20; or between 0.3 and 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.5, 2, 2.5, 3,3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 20; or between0.4 and 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6,7, 8, 9, 10, 11, 12, 13, 14, 15, or 20; or between 0.5 and 0.6, 0.7,0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, or 20; or between 0.6 and 0.7, 0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5,4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 20; or between 0.7 and0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, or 20; or between 0.8 and 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5,5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 20; or between 0.9 and 1, 1.5,2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 20; orbetween 1 and 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12,13, 14, 15, or 20; or between 1.5 and 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7,8, 9, 10, 11, 12, 13, 14, 15, or 20; or between 2 and 2.5, 3, 3.5, 4,4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 20; or between 2.5 and 3,3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 20; or between 3and 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 20; orbetween 3.5 and 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 20; orbetween 4 and 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 20; orbetween 4.5 and 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 20; or between5 and 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 20; or between 6 and 7, 8,9, 10, 11, 12, 13, 14, 15, or 20; or between 7 and 8, 9, 10, 11, 12, 13,14, 15, or 20; or between 8 and 9, 10, 11, 12, 13, 14, 15, or 20; orbetween 9 and 10, 11, 12, 13, 14, 15, or 20; or between 10 and 11, 12,13, 14, 15, or 20; or between 11 and 12, 13, 14, 15, or 20; or between12 and 13, 14, 15, or 20; or between 13 and 14, 15, or 20; or between 14and 15, or 20; or between 15 and 20; B is between 0.1 and 0.2, 0.3, 0.4,0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9,10, 11, 12, 13, 14, 15, or 20; or between 0.2 and 0.3, 0.4, 0.5, 0.6,0.7, 0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11,12, 13, 14, 15, or 20; or between 0.3 and 0.4, 0.5, 0.6, 0.7, 0.8, 0.9,1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,or 20; or between 0.4 and 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.5, 2, 2.5, 3,3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 20; or between0.5 and 0.6, 0.7, 0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8,9, 10, 11, 12, 13, 14, 15, or 20; or between 0.6 and 0.7, 0.8, 0.9, 1,1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or20; or between 0.7 and 0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6,7, 8, 9, 10, 11, 12, 13, 14, 15, or 20; or between 0.8 and 0.9, 1, 1.5,2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 20; orbetween 0.9 and 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11,12, 13, 14, 15, or 20; or between 1 and 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5,6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 20; or between 1.5 and 2, 2.5, 3,3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 20; or between 2and 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 20;or between 2.5 and 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,15, or 20; or between 3 and 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, or 20; or between 3.5 and 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, or 20; or between 4 and 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,15, or 20; or between 4.5 and 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or20; or between 5 and 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 20; orbetween 6 and 7, 8, 9, 10, 11, 12, 13, 14, 15, or 20; or between 7 and8, 9, 10, 11, 12, 13, 14, 15, or 20; or between 8 and 9, 10, 11, 12, 13,14, 15, or 20; or between 9 and 10, 11, 12, 13, 14, 15, or 20; orbetween 10 and 11, 12, 13, 14, 15, or 20; or between 11 and 12, 13, 14,15, or 20; or between 12 and 13, 14, 15, or 20; or between 13 and 14,15, or 20; or between 14 and 15, or 20; or between 15 and 20; C is,where applicable, between 0.1 and 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8,0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,15, or 20; or between 0.2 and 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.5,2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 20; orbetween 0.3 and 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4,4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 20; or between 0.4 and0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9,10, 11, 12, 13, 14, 15, or 20; or between 0.5 and 0.6, 0.7, 0.8, 0.9, 1,1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or20; or between 0.6 and 0.7, 0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5,6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 20; or between 0.7 and 0.8, 0.9,1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,or 20; or between 0.8 and 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7,8, 9, 10, 11, 12, 13, 14, 15, or 20; or between 0.9 and 1, 1.5, 2, 2.5,3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 20; or between1 and 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,15, or 20; or between 1.5 and 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10,11, 12, 13, 14, 15, or 20; or between 2 and 2.5, 3, 3.5, 4, 4.5, 5, 6,7, 8, 9, 10, 11, 12, 13, 14, 15, or 20; or between 2.5 and 3, 3.5, 4,4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 20; or between 3 and 3.5,4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 20; or between 3.5 and4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 20; or between 4 and4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 20; or between 4.5 and 5,6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 20; or between 5 and 6, 7, 8, 9,10, 11, 12, 13, 14, 15, or 20; or between 6 and 7, 8, 9, 10, 11, 12, 13,14, 15, or 20; or between 7 and 8, 9, 10, 11, 12, 13, 14, 15, or 20; orbetween 8 and 9, 10, 11, 12, 13, 14, 15, or 20; or between 9 and 10, 11,12, 13, 14, 15, or 20; or between 10 and 11, 12, 13, 14, 15, or 20; orbetween 11 and 12, 13, 14, 15, or 20; or between 12 and 13, 14, 15, or20; or between 13 and 14, 15, or 20; or between 14 and 15, or 20; orbetween 15 and 20; and D is, where applicable, between 0.1 and 0.2, 0.3,0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7,8, 9, 10, 11, 12, 13, 14, 15, or 20; or between 0.2 and 0.3, 0.4, 0.5,0.6, 0.7, 0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10,11, 12, 13, 14, 15, or 20; or between 0.3 and 0.4, 0.5, 0.6, 0.7, 0.8,0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,15, or 20; or between 0.4 and 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.5, 2, 2.5,3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 20; or between0.5 and 0.6, 0.7, 0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8,9, 10, 11, 12, 13, 14, 15, or 20; or between 0.6 and 0.7, 0.8, 0.9, 1,1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or20; or between 0.7 and 0.8, 0.9, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6,7, 8, 9, 10, 11, 12, 13, 14, 15, or 20; or between 0.8 and 0.9, 1, 1.5,2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 20; orbetween 0.9 and 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11,12, 13, 14, 15, or 20; or between 1 and 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5,6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 20; or between 1.5 and 2, 2.5, 3,3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 20; or between 2and 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 20;or between 2.5 and 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,15, or 20; or between 3 and 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, or 20; or between 3.5 and 4, 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, or 20; or between 4 and 4.5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,15, or 20; or between 4.5 and 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or20; or between 5 and 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 20; orbetween 6 and 7, 8, 9, 10, 11, 12, 13, 14, 15, or 20; or between 7 and8, 9, 10, 11, 12, 13, 14, 15, or 20; or between 8 and 9, 10, 11, 12, 13,14, 15, or 20; or between 9 and 10, 11, 12, 13, 14, 15, or 20; orbetween 10 and 11, 12, 13, 14, 15, or 20; or between 11 and 12, 13, 14,15, or 20; or between 12 and 13, 14, 15, or 20; or between 13 and 14,15, or 20; or between 14 and 15, or 20; or between 15 and 20. In someembodiments, A, B, and/or C is within rounding of any of these values(e.g., A is between 0.45 and 0.54, etc.).

In some embodiments the patient's percentage risk (absolute or relative)of a particular clinical event or outcome (e.g., cancer-specific death,recurrence after surgery, etc.) is estimated (e.g., calculated)according to the disclosure (e.g., according to one or more of theformulae above). Such risk may be estimated by applying the hazard ratiofor a particular parameter (e.g., CCP score, Combined Score) to thatparameter to yield a patient's relative risk of a particular clinicaloutcome (e.g., cancer recurrence or cancer-specific death). In somecases, the hazard ratio represents the relative risk increase per unitof the parameter. In some of the examples below, for instance, a singleunit increase in CCP score (which represents a doubling of expression)represents a relative risk increased by the multiple of the hazardration. Where the hazard ratio is equal to 2, for example, a single unitincrease in CCP score corresponds to a doubling of relative risk (i.e.,a first patient with a CCP score that is one unit higher than a secondpatient has twice the risk of cancer recurrence or cancer-specificdeath). This relative risk can be used with the average risk in aparticular population to determine how a specific patient's riskcompares to such population. One way to do this is to set the averagevalue of the parameter in the population as zero and then comparespecific patient's values for the parameter, meaning a patient with,e.g., a CCP score of 1 would have double the average risk of cancerrecurrence or cancer-specific death.

Some embodiments of the disclosure, therefore, provide a method ofcalculating a patient's risk of cancer recurrence or cancer-specificdeath comprising (1) obtaining the measured expression levels of aplurality of genes comprising at least 3 genes chosen from any of Tables1, 2, 7-11, 13-14 and/or Y or Panels A through I in a sample from thepatient, (2) calculating a test value from these measured expressionlevels as discussed herein (e.g., CCP genes contributing at least someweight, at least some number of CCP genes, etc.), and (3) calculatingsaid patient's risk of cancer recurrence or cancer-specific death bymultiplying the number of increased units of the test value over somereference value (e.g., average values in a particular population) by thehazard ratio for the value. In some embodiments, the test valuecomprises the CCP score or a Combined Score as described herein and thehazard ration is any of the hazard ratios reported herein.

A more absolute (rather than relative) risk of recurrence may also beestimated by gathering data from a study patient cohort and correlatingtest values and scores for such patients with their eventual clinicalevents or outcomes. Such data may be used in a graphical form (FIGS. 23& 24), tabular form, or as embodied in a formula (e.g., formula (4)below) to, based on a test patient's score, determine such testpatient's risk of the particular clinical event or outcome. For example,one may measure a patient's CCP Score as 1.7, calculate a patient'sCAPRA score as 5, and then calculate the patient's (e.g., biopsy)Combined Score using formula (2), with A=0.57 & B=0.39, as 2.92. One maythen use this Combined Score to calculate such patient's risk ofcancer-specific death within 10 years by, e.g., using a pre-specifiedformula (e.g., formula (4)), using a curve (e.g., FIG. 23 or 24), or arisk table. In some embodiments, the risk is anything within the 95%confidence interval, e.g., the intervals shown in FIG. 23 or 24.

Using these empirical data (e.g., those embodied in FIGS. 23 & 24), onemay derive formulae of the following general form to estimate risk:Estimated Risk of A=B*e ^(C*D)  (4)Often, these formulae will be derived by plotting risk versus CCP Scoreor Combined Score for a set of study patient samples and fitting a curveto the resultant line (e.g., one of the lines shown in FIG. 24). In someembodiments, A is cancer-specific death or biochemical recurrence. Insome embodiments, D is CCP score or a Combined Score (each as describedin the various aspects and embodiments herein). In some embodimentsB=0.0155 & C=0.0054 (as derived from, e.g., a line as shown in FIG. 24).In such a case, formula (4) would be modified as follows:Estimated Risk of Cancer-Specific Death=0.0155*e^(0.0054*(Combined score))  (5)where the Combined Score is calculated according to any of the formulaediscussed herein. In some such specific embodiments, the Combined Scoreis calculated according to formula (2) with A=0.57 & B=0.39 and theclinical score being the CAPRA score.

Thus, in some embodiments the disclosure provides a method ofcalculating a patient's risk of prostate cancer-specific deathcomprising: (1) obtaining the measured expression levels of a pluralityof genes comprising at least 4 genes from any of Tables 1, 2, 7-11,13-14 and/or Y or Panels A through I; (2) optionally obtaining a scorefor the patient calculated from at least one clinical variable (e.g.,one or more of year of RP, surgical margins, extracapsular extension,seminal vesicle invasion, lymph node involvement, primary Gleason score,secondary Gleason score, or preoperative PSA level); (3) optionallyderiving a combined test value from the measured levels obtained in (1)and the score obtained in (2); (4) and calculating the patient's risk ofprostate cancer-specific death according to the following formula:Risk of Cancer-Specific Death=0.0155e*^(0.0054*([Measured expression levels in (1)] or [Combined Score obtained in (2)]))

In some embodiments the disclosure provides a method of calculating apatient's risk of prostate cancer-specific death comprising: (1)obtaining the measured expression levels of a plurality of genescomprising at least 4 genes from any of Tables 1, 2, 7-11, 13-14 and/orY or Panels A through I; (2) optionally obtaining a CAPRA score for thepatient sample as discussed herein; (3) optionally deriving a combinedtest value from the measured levels obtained in (1) and the scoreobtained in (2) according to the formula: Combined Score=(0.57*(Score in(2))+(0.39*Score in (1)); (4) and calculating the patient's risk ofprostate cancer-specific death according to the table in FIG. 26.

In some embodiments, the test value derived or calculated from aparticular gene (e.g., KLK3) or from the overall expression of theplurality of test genes (e.g., CCGs) is compared to one or morereference values (or index values), and the test value is optionallycorrelated to prognosis, risk of cancer progression, risk of cancerrecurrence, or risk of cancer-specific death if it differs from theindex value.

For example, the index value may be derived or calculated from the geneexpression levels found in a normal sample obtained from the patient ofinterest, in which case a test value (derived or calculated from anexpression level in the tumor sample) significantly higher than thisindex value would indicate, e.g., a poor prognosis or increasedlikelihood of cancer recurrence or cancer-specific death or a need foraggressive treatment. In some embodiments the test value is deemed“greater than” the reference value (e.g., the threshold index value),and thus correlated to an increased likelihood of response to treatmentcomprising chemotherapy, if the test value exceeds the reference valueby at least some amount (e.g., at least 0.5, 0.75, 0.85, 0.90, 0.95, 1,2, 3, 4, 5, 6, 7, 8, 9, or 10 or more fold or standard deviations).

Alternatively, the index value may be derived or calculated from theaverage expression level of for a set of individuals from a diversecancer population or a subset of the population. For example, one maydetermine the average expression level of a gene or gene panel in arandom sampling of patients with cancer (e.g., prostate, bladder, brain,breast, or lung cancer). This average expression level may be termed the“threshold index value,” with patients having CCG expression higher thanthis value expected to have a poorer prognosis than those havingexpression lower than this value.

Alternatively the index value may be derived or calculated from a mixedcohort of high and low risk individuals such that the index valuerepresents a threshold for active surveillance versus treatment. Theindex value may be based on the expression of an individual gene, apanel of genes, or a combined score incorporating gene expression andother clinical parameters as described herein. Individuals whose geneexpression or combined score is less than or equal to the thresholdwould qualify for active surveillance based on a lower risk ofmortality, whereas those with gene expression or a combined score higherthan the threshold would not qualify based on higher risk of mortality.In some embodiments, the threshold is based on a combined score. In someembodiments, the threshold for the combined score is between about 0.6and about 0.8. In other embodiments, the threshold is between 0.6 and0.8. In other embodiments, the threshold is 0.6, 0.7 or 0.8. In otherembodiments, the threshold is 0.6, 0.61, 0.62, 0.63, 0.64, 0.65, 0.66,0.67, 0.68, 0.69, 0.7, 0.71, 0.72, 0.73, 0.74, 0.75, 0.76, 0.77, 0.78,0.79, or 0.8.

Alternatively the index value may represent the average expression levelof a particular gene marker or plurality of markers in a plurality oftraining patients (e.g., prostate cancer patients) with similar outcomeswhose clinical and follow-up data are available and sufficient to defineand categorize the patients by disease outcome, e.g., recurrence orprognosis. See, e.g., Examples, infra. For example, a “good prognosisindex value” can be generated from a plurality of training cancerpatients characterized as having “good outcome”, e.g., those who havenot had cancer recurrence five years (or ten years or more) afterinitial treatment, or who have not had progression in their cancer fiveyears (or ten years or more) after initial diagnosis. A “poor prognosisindex value” can be generated from a plurality of training cancerpatients defined as having “poor outcome”, e.g., those who have hadcancer recurrence within five years (or ten years, etc.) after initialtreatment, or who have had progression in their cancer within five years(or ten years, etc.) after initial diagnosis. Thus, a good prognosisindex value of a particular gene may represent the average level ofexpression of the particular gene in patients having a “good outcome,”whereas a poor prognosis index value of a particular gene represents theaverage level of expression of the particular gene in patients having a“poor outcome.”

Thus one aspect of the disclosure provides a method of classifyingcancer comprising determining the status of a panel of genes comprisingat least two CCGs, in tissue or cell sample, particularly a tumorsample, from a patient, wherein an abnormal status indicates a negativecancer classification. As used herein, “determining the status” of agene refers to determining the presence, absence, or extent/level ofsome physical, chemical, or genetic characteristic of the gene or itsexpression product(s). Such characteristics include, but are not limitedto, expression levels, activity levels, mutations, copy number,methylation status, etc.

In the context of CCGs as used to determine risk of cancer recurrence orprogression or need for aggressive treatment, particularly usefulcharacteristics include expression levels (e.g., mRNA or protein levels)and activity levels. Characteristics may be assayed directly (e.g., byassaying a CCG's expression level) or determined indirectly (e.g.,assaying the level of a gene or genes whose expression level iscorrelated to the expression level of the CCG). Thus some embodiments ofthe disclosure provide a method of classifying cancer comprisingdetermining the expression level, particularly mRNA level of a panel ofgenes comprising at least two CCGs, in a tumor sample, wherein highexpression (or increased expression or overexpression) indicates anegative cancer classification, or an increased risk of cancerrecurrence or progression, or a need for aggressive treatment. In someembodiments, the method comprises at least one of the following steps:(a) correlating high expression (or increased expression oroverexpression) of the panel of genes to a negative cancerclassification, an increased risk of cancer recurrence or progression,or a need for aggressive treatment; (b) concluding that the patient hasa negative cancer classification, an increased risk of cancer recurrenceor progression, or a need for aggressive treatment based at least inpart on high expression (or increased expression or overexpression) ofthe panel of genes; or (c) communicating that the patient has a negativecancer classification, an increased risk of cancer recurrence orprogression, or a need for aggressive treatment based at least in parton high expression (or increased expression or overexpression) of thepanel of genes.

“Abnormal status” means a marker's status in a particular sample differsfrom the status generally found in average samples (e.g., healthysamples or average diseased samples). Examples include mutated,elevated, decreased, present, absent, etc. An “elevated status” meansthat one or more of the above characteristics (e.g., expression or mRNAlevel) is higher than normal levels. Generally this means an increase inthe characteristic (e.g., expression or mRNA level) as compared to anindex value. Conversely a “low status” means that one or more of theabove characteristics (e.g., gene expression or mRNA level) is lowerthan normal levels. Generally this means a decrease in thecharacteristic (e.g., expression) as compared to an index value. In thiscontext, a “negative status” generally means the characteristic isabsent or undetectable. For example, PTEN status is negative if PTENnucleic acid and/or PTEN protein is absent or undetectable in a sample.However, negative PTEN status also includes a mutation or copy numberreduction in PTEN.

In some embodiments of the disclosure the methods comprise determiningthe expression of one or more CCGs and, if this expression is“increased,” the patient has a poor prognosis. In the context of thedisclosure, “increased” expression of a CCG means the patient'sexpression level is either elevated over a normal index value or athreshold index (e.g., by at least some threshold amount) or closer tothe “poor prognosis index value” than to the “good prognosis indexvalue.”

Thus, when the determined level of expression of a relevant gene markeris closer to the good prognosis index value of the gene than to the poorprognosis index value of the gene, then it can be concluded that thepatient is more likely to have a good prognosis, i.e., a low (or noincreased) likelihood of cancer recurrence. On the other hand, if thedetermined level of expression of a relevant gene marker is closer tothe poor prognosis index value of the gene than to the good prognosisindex value of the gene, then it can be concluded that the patient ismore likely to have a poor prognosis, i.e., an increased likelihood ofcancer recurrence.

Alternatively index values may be determined thusly: In order to assignpatients to risk groups, a threshold value will be set for the cellcycle mean. The optimal threshold value is selected based on thereceiver operating characteristic (ROC) curve, which plots sensitivityvs (1−specificity). For each increment of the cell cycle mean, thesensitivity and specificity of the test is calculated using that valueas a threshold. The actual threshold will be the value that optimizesthese metrics according to the artisans requirements (e.g., what degreeof sensitivity or specificity is desired, etc.). Example 5 demonstratesdetermination of a threshold value determined and validatedexperimentally.

Panels of CCGs (e.g., 2, 3, 4, 5, 6, 7, 8, 9, or 10 or more CCGs) canaccurately predict prognosis, as shown in Example 3. Those skilled inthe art are familiar with various ways of determining the expression ofa panel of genes (i.e., a plurality of genes). One may determine theexpression of a panel of genes by determining the average expressionlevel (normalized or absolute) of all panel genes in a sample obtainedfrom a particular patient (either throughout the sample or in a subsetof cells from the sample or in a single cell). Increased expression inthis context will mean the average expression is higher than the averageexpression level of these genes in normal patients (or higher than someindex value that has been determined to represent the average expressionlevel in a reference population such as patients with the same cancer).Alternatively, one may determine the expression of a panel of genes bydetermining the average expression level (normalized or absolute) of atleast a certain number (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25,30 or more) or at least a certain proportion (e.g., 10%, 20%, 30%, 40%,50%, 60%, 70%, 80%, 90%, 95%, 99%, 100%) of the genes in the panel.Alternatively, one may determine the expression of a panel of genes bydetermining the absolute copy number of the mRNA (or protein) of all thegenes in the panel and either total or average these across the genes.

As used herein, “classifying a cancer” and “cancer classification” referto determining one or more clinically-relevant features of a cancerand/or determining a particular prognosis of a patient having saidcancer. Thus “classifying a cancer” includes, but is not limited to: (i)evaluating metastatic potential, potential to metastasize to specificorgans, risk of recurrence, and/or course of the tumor; (ii) evaluatingtumor stage; (iii) determining patient prognosis in the absence oftreatment of the cancer; (iv) determining prognosis of patient response(e.g., tumor shrinkage or progression-free survival) to treatment (e.g.,chemotherapy, radiation therapy, surgery to excise tumor, etc.); (v)diagnosis of actual patient response to current and/or past treatment;(vi) determining a preferred course of treatment for the patient; (vii)prognosis for patient relapse after treatment (either treatment ingeneral or some particular treatment); (viii) prognosis of patient lifeexpectancy (e.g., prognosis for overall survival), etc.

Thus, a “negative classification” means an unfavorable clinical featureof the cancer (e.g., a poor prognosis). Examples include (i) anincreased metastatic potential, potential to metastasize to specificorgans, and/or risk of recurrence; (ii) an advanced tumor stage; (iii) apoor patient prognosis in the absence of treatment of the cancer; (iv) apoor prognosis of patient response (e.g., tumor shrinkage orprogression-free survival) to a particular treatment (e.g.,chemotherapy, radiation therapy, surgery to excise tumor, etc.); (v) apoor prognosis for patient relapse after treatment (either treatment ingeneral or some particular treatment); (vi) a poor prognosis of patientlife expectancy (e.g., prognosis for overall survival), etc. In someembodiments a recurrence-associated clinical parameter (or a highnomogram score) and increased expression of a CCG indicate a negativeclassification in cancer (e.g., increased likelihood of recurrence orprogression).

A patient with a sample showing a high CCP score or value (or increasedCCP expression) has an increased likelihood of recurrence aftertreatment (e.g., the cancer cells not killed or removed by the treatmentwill quickly grow back). Such a patient also has an increased likelihoodof cancer progression for more rapid progression (e.g., the rapidlyproliferating cells will cause any tumor to grow quickly, gain invirulence, and/or metastasize). Such a patient may also require arelatively more aggressive treatment. Thus, in some embodiments thedisclosure provides a method of classifying cancer comprisingdetermining the status of a panel of genes comprising at least two CCGs,wherein an abnormal status indicates an increased likelihood ofrecurrence or progression. In some embodiments, the method comprises atleast one of the following steps: (a) correlating abnormal status of thepanel of genes to an increased likelihood of recurrence or progression;(b) concluding that the patient has an increased likelihood ofrecurrence or progression based at least in part on abnormal status ofthe panel of genes; or (c) communicating that the patient has anincreased likelihood of recurrence or progression based at least in parton abnormal status of the panel of genes. As discussed above, in someembodiments the status to be determined is gene expression levels. Thusin some embodiments the disclosure provides a method of determining theprognosis of a patient's cancer comprising determining the expressionlevel of a panel of genes comprising at least two CCGs, wherein highexpression (or increased expression or overexpression) indicates anincreased likelihood of recurrence or progression of the cancer. In someembodiments, the method comprises at least one of the following steps:(a) correlating high expression (or increased expression oroverexpression) of the panel of genes to an increased likelihood ofrecurrence or progression; (b) concluding that the patient has anincreased likelihood of recurrence or progression based at least in parton high expression (or increased expression or overexpression) of thepanel of genes; or (c) communicating that the patient has an increasedlikelihood of recurrence or progression based at least in part on highexpression (or increased expression or overexpression) of the panel ofgenes.

“Recurrence” and “progression” are terms well-known in the art and areused herein according to their known meanings. Because the methods ofthe disclosure can predict or determine a patient's likelihood of each,“recurrence,” “progression,” “cancer-specific death,” and “response to aparticular treatment” are used interchangeably, unless specifiedotherwise, in the sense that a reference to one applies equally to theothers. As an example, the meaning of “progression” may be cancer-typedependent, with progression in lung cancer meaning something differentfrom progression in prostate cancer. However, within each cancer-typeand subtype “progression” is clearly understood to those skilled in theart. Because predicting recurrence and predicting progression areprognostic endeavors, “predicting prognosis” will often be used hereinto refer to either or both. In these cases, a “poor prognosis” willgenerally refer to an increased likelihood of recurrence, progression,or both.

“Response” (e.g., response to a particular treatment regimen) is awell-known term in the art and is used herein according to its knownmeaning. As an example, the meaning of “response” may be cancer-typedependent, with response in lung cancer meaning something different fromresponse in prostate cancer. However, within each cancer-type andsubtype “response” is clearly understood to those skilled in the art.For example, some objective criteria of response include ResponseEvaluation Criteria In Solid Tumors (RECIST), a set of published rules(e.g., changes in tumor size, etc.) that define when cancer patientsimprove (“respond”), stay the same (“stabilize”), or worsen(“progression”) during treatments. See, e.g., Eisenhauer et al., EUR. J.CANCER (2009) 45:228-247. “Response” can also include survival metrics(e.g., “disease-free survival” (DFS), “overall survival” (OS), etc). Insome cases RECIST criteria can include: (a) Complete response (CR):disappearance of all metastases; (b) Partial response (PR): at least a30% decrease in the sum of the largest diameter (LD) of the metastaticlesions, taking as reference the baseline sum LD; (c) Stable disease(SD): neither sufficient shrinkage to qualify for PR nor sufficientincrease to qualify for PD taking as references the smallest sum LDsince the treatment started; (d) Progression (PD): at least a 20%increase in the sum of the LD of the target metastatic lesions taking asreference the smallest sum LD since the treatment started or theappearance of one or more new lesions.

As used herein, a patient has an “increased likelihood” of some clinicalfeature or outcome (e.g., recurrence or progression) if the probabilityof the patient having the feature or outcome exceeds some referenceprobability or value. The reference probability may be the probabilityof the feature or outcome across the general relevant patientpopulation. For example, if the probability of recurrence in the generalprostate cancer population is X % and a particular patient has beendetermined by the methods of the present disclosure to have aprobability of recurrence of Y %, and if Y>X, then the patient has an“increased likelihood” of recurrence. Alternatively, as discussed above,a threshold or reference value may be determined and a particularpatient's probability of recurrence may be compared to that threshold orreference.

In some embodiments the method correlates the patient's specific score(e.g., CCP score, combined score of CCP with clinical variables) to aspecific probability (e.g., 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%,55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99%, 100%) of recurrence,progression, or cancer-specific death (each optionally within a specifictimeframe, e.g., 5 years, 10 years), or response to a particulartreatment. In some embodiments the disclosure provides a method fordetermining a prostate cancer patient's prognosis comprising: (1)determining from a patient sample the expression levels of a pluralityof test genes, wherein the plurality of test genes comprises at least 5of the genes in any one of Panels A to G; (2) deriving a test value fromthe expression levels determined in (1), wherein the at least 5 genes inany one of Panels A to G contribute at least 25% to the test value; (3)comparing the test value to a reference value; and (4) assigning alikelihood of recurrence, progression, cancer-specific death, orresponse to a particular treatment based at least in part on thecomparison in (3).

In some embodiments, the patient sample is from a prostate biopsy, thetest value is the mean C_(T) for the genes in Panel F normalized againstthe genes in Table 3, and the likelihood of prostate cancer-specificdeath within 10 years of diagnosis is calculated as follows:

TABLE 4 Test Likelihood of Cancer- Value Specific Death −1  5.9% 0 11.6%1  22% 2 39.5% 3 63.8% 4 87.2%

In some embodiments, the patient sample is from a prostatectomy, thetest value is the mean C_(T) for the genes in Panel F normalized againstthe genes in Table A, and the likelihood of prostate cancer recurrencewithin 10 years of surgery is calculated as follows:

TABLE 5 Test Likelihood of Value Recurrence −1 12.6% 0 24.9% 1 45.5% 272.5% 3 93.6%

In some embodiments, the patient sample is from a prostatectomy, thetest value is a combined score calculated as shown in paragraphs [0067]& [0068] above, and the likelihood of prostate cancer recurrence within10 years of surgery is calculated as follows:

TABLE 6 Test Likelihood of Value Recurrence 0 11.5% 1  25% 2 49.3% 379.8% 4 97.7%

As shown in Example 3, individual CCGs can predict prognosis quite well.Thus the disclosure provides a method of predicting prognosis comprisingdetermining the expression of at least one CCG listed in Table 1 orPanels A through G.

Example 3 also shows that panels of CCGs (e.g., 2, 3, 4, 5, or 6 CCGs)can accurately predict prognosis. Thus in some aspects the disclosureprovides a method of classifying a cancer comprising determining thestatus of a panel of genes (e.g., a plurality of test genes) comprisinga plurality of CCGs. For example, increased expression in a panel ofgenes (or plurality of test genes) may refer to the average expressionlevel of all panel or test genes in a particular patient being higherthan the average expression level of these genes in normal patients (orhigher than some index value that has been determined to represent thenormal average expression level). Alternatively, increased expression ina panel of genes may refer to increased expression in at least a certainnumber (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30 or more) orat least a certain proportion (e.g., 10%, 20%, 30%, 40%, 50%, 60%, 70%,80%, 90%, 95%, 99%, 100%) of the genes in the panel as compared to theaverage normal expression level.

In some embodiments the panel comprises at least 3, 4, 5, 6, 7, 8, 9,10, 15, 20, 25, 30, 35, 40, 45, 50, 70, 80, 90, 100, 200, or more CCGs.In some embodiments the panel comprises at least 10, 15, 20, or moreCCGs. In some embodiments the panel comprises between 5 and 100 CCGs,between 7 and 40 CCGs, between 5 and 25 CCGs, between 10 and 20 CCGs, orbetween 10 and 15 CCGs. In some embodiments CCGs comprise at least acertain proportion of the panel. Thus in some embodiments the panelcomprises at least 25%, 30%, 40%, 50%, 60%, 70%, 75%, 80%, 85%, 90%,95%, 96%, 97%, 98%, or 99% CCGs. In some preferred embodiments the panelcomprises at least 10, 15, 20, 25, 30, 35, 40, 45, 50, 70, 80, 90, 100,200, or more CCGs, and such CCGs constitute of at least 50%, 60%, 70%,preferably at least 75%, 80%, 85%, more preferably at least 90%, 95%,96%, 97%, 98%, or 99% or more of the total number of genes in the panel.In some embodiments the CCGs are chosen from the group consisting of thegenes in Table 1 and Panels A through G. In some embodiments the panelcomprises at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20,25, 30, or more of the genes in any of Table 1 and Panels A through G.In some embodiments the disclosure provides a method of predictingprognosis comprising determining the status of the CCGs in Panels Athrough G, wherein abnormal status indicates a poor prognosis. In someembodiments, the method comprises at least one of the following steps:(a) correlating abnormal status (e.g., high or increased expression) ofthe CCGs in Panels A through G to a poor prognosis; (b) concluding thatthe patient has a poor prognosis based at least in part on abnormalstatus (e.g., high or increased expression) of the CCGs in Panels Athrough G; or (c) communicating that the patient has a poor prognosisbased at least in part on abnormal status (e.g., high or increasedexpression) of the CCGs in Panels A through G.

In some of these embodiments elevated expression indicates an increasedlikelihood of recurrence or progression. Thus in a preferred embodimentthe disclosure provides a method of predicting risk of cancer recurrenceor progression in a patient comprising determining the status of a panelof genes, wherein the panel comprises between about 10 and about 15CCGs, the CCGs constitute at least 90% of the panel, and an elevatedstatus for the CCGs indicates an increased likelihood or recurrence orprogression. In some embodiments, the method comprises at least one ofthe following steps: (a) correlating elevated status (e.g., high orincreased expression) of the panel of genes to a poor prognosis; (b)concluding that the patient has a poor prognosis based at least in parton elevated status (e.g., high or increased expression) of the panel ofgenes; or (c) communicating that the patient has a poor prognosis basedat least in part on elevated status (e.g., high or increased expression)of the panel of genes.

Several panels of CCGs (Table 2, supra, and Tables 7 & 8, infra) havebeen evaluated for their ability to predict prognosis in severaldifferent cancers. The results of these studies are described inExamples 1 through 6 below.

TABLE 7 “Panel C” Evaluated in Examples 1 through 4 Gene Entrez SymbolGeneID AURKA 6790 BUB1* 699 CCNB1* 891 CCNB2* 9133 CDC2* 983 CDC20* 991CDC45L* 8318 CDCA8* 55143 CENPA 1058 CKS2* 1164 DLG7* 9787 DTL* 51514FOXM1* 2305 HMMR* 3161 KIF23* 9493 KPNA2 3838 MAD2L1* 4085 MELK 9833MYBL2* 4605 NUSAP1* 51203 PBK* 55872 PRC1* 9055 PTTG1* 9232 RRM2* 6241TIMELESS* 8914 TPX2* 22974 TRIP13* 9319 TTK* 7272 UBE2C 11065 UBE2S*27338 ZWINT* 11130 *These genes were used as a 26-gene subset panel(“Panel D”) in the validation arm of the experiment described in Example2.

TABLE 8 “Panel E” Name GeneID ASF1B* 55723 ASPM* 259266 BIRC5* 332BUB1B* 701 C18orf24* 220134 CDC2* 983 CDC20* 991 CDCA3* 83461 CDCA8*55143 CDKN3* 1033 CENPF* 1063 CENPM* 79019 CEP55* 55165 DLGAP5* 9787DTL* 51514 FOXM1* 2305 KIAA0101* 9768 KIF11* 3832 KIF20A* 10112 KIF4A24137 MCM10* 55388 NUSAP1* 51203 ORC6L* 23594 PBK* 55872 PLK1* 5347PRC1* 9055 PTTG1* 9232 RAD51* 5888 RAD54L* 8438 RRM2* 6241 TK1* 7083TOP2A* 7153 *These genes were used as a 31-gene subset panel (“Panel F”)in the experiment described in Example 5.

It has been determined that the choice of individual CCGs for a panelcan often be relatively arbitrary. In other words, most CCGs have beenfound to be very good surrogates for each other. One way of assessingwhether particular CCGs will serve well in the methods and compositionsof the disclosure is by assessing their correlation with the meanexpression of CCGs (e.g., all known CCGs, a specific set of CCGs, etc.).Those CCGs that correlate particularly well with the mean are expectedto perform well in assays of the disclosure, e.g., because these willreduce noise in the assay. A ranking of select CCGs according to theircorrelation with the mean CCG expression is given in Tables 9-11.

In CCG signatures the particular CCGs assayed is often not as importantas the total number of CCGs. The number of CCGs assayed can varydepending on many factors, e.g., technical constraints, costconsiderations, the classification being made, the cancer being tested,the desired level of predictive power, etc. Increasing the number ofCCGs assayed in a panel according to the disclosure is, as a generalmatter, advantageous because, e.g., a larger pool of mRNAs to be assayedmeans less “noise” caused by outliers and less chance of an assay errorthrowing off the overall predictive power of the test. However, cost andother considerations will generally limit this number and finding theoptimal number of CCGs for a signature is desirable.

It has been discovered that the predictive power of a CCG signatureoften ceases to increase significantly beyond a certain number of CCGs(see FIG. 1; Example 1). More specifically, the optimal number of CCGsin a signature (n_(O)) can be found wherever the following is true(P _(n+1) −P _(n))<C _(O),wherein P is the predictive power (i.e., P, is the predictive power of asignature with n genes and P_(n+1) is the predictive power of asignature with n genes plus one) and C_(O) is some optimizationconstant. Predictive power can be defined in many ways known to thoseskilled in the art including, but not limited to, the signature'sp-value. C_(O) can be chosen by the artisan based on his or her specificconstraints. For example, if cost is not a critical factor and extremelyhigh levels of sensitivity and specificity are desired, C_(O) can be setvery low such that only trivial increases in predictive power aredisregarded. On the other hand, if cost is decisive and moderate levelsof sensitivity and specificity are acceptable, C_(O) can be set highersuch that only significant increases in predictive power warrantincreasing the number of genes in the signature.

Alternatively, a graph of predictive power as a function of gene numbermay be plotted (as in FIG. 1) and the second derivative of this plottaken. The point at which the second derivative decreases to somepredetermined value (C_(O)′) may be the optimal number of genes in thesignature.

Examples 1 & 3 and FIGS. 1 & 17 illustrate the empirical determinationof optimal numbers of CCGs in CCG panels of the disclosure. Randomlyselected subsets of the 31 CCGs listed in Table 7 were tested asdistinct CCG signatures and predictive power (i.e., p-value) wasdetermined for each. As FIG. 1 shows, p-values ceased to improvesignificantly between about 10 and about 15 CCGs, thus indicating thatan optimal number of CCGs in a prognostic panel is from about 10 toabout 15. Thus some embodiments of the disclosure provide a method ofpredicting prognosis in a patient having prostate cancer comprisingdetermining the status of a panel of genes, wherein the panel comprisesbetween about 10 and about 15 CCGs and an elevated status for the CCGsindicates a poor prognosis. In some embodiments, the method comprises atleast one of the following steps: (a) correlating elevated status (e.g.,high or increased expression) of the panel of genes to a poor prognosis;(b) concluding that the patient has a poor prognosis based at least inpart on elevated status (e.g., high or increased expression) of thepanel of genes; or (c) communicating that the patient has a poorprognosis based at least in part on elevated status (e.g., high orincreased expression) of the panel of genes. In some embodiments thepanel comprises between about 10 and about 15 CCGs and the CCGsconstitute at least 90% of the panel. In other embodiments the panelcomprises CCGs plus one or more additional markers that significantlyincrease the predictive power of the panel (i.e., make the predictivepower significantly better than if the panel consisted of only theCCGs). Any other combination of CCGs (including any of those listed inTable 1 or Panels A through G) can be used to practice the disclosure.

It has been discovered that CCGs are particularly predictive in certaincancers. For example, panels of CCGs have been determined to be accuratein predicting recurrence in prostate cancer (Examples 1 through 5).Further, CCGs can determine prognosis in bladder, brain, breast and lungcancers, as summarized in Example 6 below.

Thus the disclosure provides a method comprising determining the statusof a panel of genes comprising at least two CCGs, wherein an abnormalstatus indicates a poor prognosis. In some embodiments the panelcomprises at least 2 genes chosen from the group of genes in at leastone of Panels A through G. In some embodiments the panel comprises atleast 10 genes chosen from the group of genes in at least one of PanelsA through G. In some embodiments the panel comprises at least 15 geneschosen from the group of genes in at least one of Panels A through G. Insome embodiments the panel comprises all of the genes in at least one ofPanels A through G. The disclosure also provides a method of determiningthe prognosis of bladder cancer, comprising determining the status of apanel of genes comprising at least two CCGs (e.g., at least two of thegenes in any of Panels B, C, & F), wherein an abnormal status indicatesa poor prognosis. The disclosure also provides a method of determiningthe prognosis of brain cancer, comprising determining the status of apanel of genes comprising at least two CCGs (e.g., at least two of thegenes in any of Panels B, C, & F), wherein an abnormal status indicatesa poor prognosis. The disclosure further provides a method ofdetermining the prognosis of breast cancer, comprising determining thestatus of a panel of genes comprising at least two CCGs (e.g., at leasttwo of the genes in any of Panels B, C, & F), wherein an abnormal statusindicates a poor prognosis. The disclosure also provides a method ofdetermining the prognosis of lung cancer, comprising determining thestatus of a panel of genes comprising at least two CCGs (e.g., at leasttwo of the genes in any of Panels B, C, & F), wherein an abnormal statusindicates a poor prognosis. In some embodiments, the method comprises atleast one of the following steps: (a) correlating abnormal status (e.g.,high or increased expression) of the panel of genes to a poor prognosis;(b) concluding that the patient has a poor prognosis based at least inpart on abnormal status (e.g., high or increased expression) of thepanel of genes; or (c) communicating that the patient has a poorprognosis based at least in part on high expression (or increasedexpression or overexpression) of the panel of genes.

In some embodiments the panel comprises at least 3, 4, 5, 6, 7, 8, 9,10, 15, 20, 25, 30, 35, 40, 45, 50 or more CCGs. In some embodiments thepanel comprises between 5 and 100 CCGs, between 7 and 40 CCGs, between 5and 25 CCGs, between 10 and 20 CCGs, or between 10 and 15 CCGs. In someembodiments CCGs comprise at least a certain proportion of the panel.Thus in some embodiments the panel comprises at least 25%, 30%, 40%,50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% CCGs. Insome embodiments the CCGs are chosen from the group consisting of thegenes listed in Tables 1, 2, 7-11, 13-14 and/or Y and Panels A throughI. In some embodiments the panel comprises at least 2, 3, 4, 5, 6, 7, 8,9, 10, 15, 20, 25, 30, 35, 40, 45, 50 or more genes chosen from thegroup of genes in any of Tables 1, 2, 7-11, 13-14 and/or Y or Panels Athrough I. In some embodiments the panel comprises all of the genes inany of Tables 1, 2, 7-11, 13-14 and/or Y or Panels A through I.

As mentioned above, many of the CCGs of the disclosure have beenanalyzed to determine their correlation to the CCG mean and also todetermine their relative predictive value within a panel (see Tables9-11, & 13-14). The following tables rank CCGs according to thesecriteria.

Tables 9-11 below provide rankings of select CCGs according to theircorrelation with the mean CCG expression. Table 9 provides a ranking ofselect control genes according to their correlation to the control meanexpression.

TABLE 9 Gene # Gene Symbol Correl. w/Mean 1 TPX2 0.931 2 CCNB2 0.9287 3KIF4A 0.9163 4 KIF2C 0.9147 5 BIRC5 0.9077 6 BIRC5 0.9077 7 RACGAP10.9073 8 CDC2 0.906 9 PRC1 0.9053 10 DLGAP5 (DLG7) 0.9033 11 CEP55 0.90312 CCNB1 0.9 13 TOP2A 0.8967 14 CDC20 0.8953 15 KIF20A 0.8927 16 BUB1B0.8927 17 CDKN3 0.8887 18 NUSAP1 0.8873 19 CCNA2 0.8853 20 KIF11 0.872321 CDCA8 0.8713 22 NCAPG 0.8707 23 ASPM 0.8703 24 FOXM1 0.87 25 NEK20.869 26 ZWINT 0.8683 27 PTTG1 0.8647 28 RRM2 0.8557 29 TTK 0.8483 30TRIP13 0.841 31 GINS1 0.841 32 CENPF 0.8397 33 HMMR 0.8367 34 NCAPH0.8353 35 NDC80 0.8313 36 KIF15 0.8307 37 CENPE 0.8287 38 TYMS 0.8283 39KIAA0101 0.8203 40 FANCI 0.813 41 RAD51AP1 0.8107 42 CKS2 0.81 43 MCM20.8063 44 PBK 0.805 45 ESPL1 0.805 46 MKI67 0.7993 47 SPAG5 0.7993 48MCM10 0.7963 49 MCM6 0.7957 50 OIP5 0.7943 51 CDC45L 0.7937 52 KIF230.7927 53 EZH2 0.789 54 SPC25 0.7887 55 STIL 0.7843 56 CENPN 0.783 57GTSE1 0.7793 58 RAD51 0.779 59 CDCA3 0.7783 60 TACC3 0.778 61 PLK40.7753 62 ASF1B 0.7733 63 DTL 0.769 64 CHEK1 0.7673 65 NCAPG2 0.7667 66PLK1 0.7657 67 TIMELESS 0.762 68 E2F8 0.7587 69 EXO1 0.758 70 ECT2 0.74471 STMN1 0.737 72 STMN1 0.737 73 RFC4 0.737 74 CDC6 0.7363 75 CENPM0.7267 76 MYBL2 0.725 77 SHCBP1 0.723 78 ATAD2 0.723 79 KIFC1 0.7183 80DBF4 0.718 81 CKS1B 0.712 82 PCNA 0.7103 83 FBXO5 0.7053 84 C12orf480.7027 85 TK1 0.7017 86 BLM 0.701 87 KIF18A 0.6987 88 DONSON 0.688 89MCM4 0.686 90 RAD54B 0.679 91 RNASEH2A 0.6733 92 TUBA1C 0.6697 93C18orf24 0.6697 94 SMC2 0.6697 95 CENPI 0.6697 96 GMPS 0.6683 97 DDX390.6673 98 POLE2 0.6583 99 APOBEC3B 0.6513 100 RFC2 0.648 101 PSMA70.6473 102 KIF20B (MPHOSPH1) 0.6457 103 CDT1 0.645 104 H2AFX 0.6387 105ORC6L 0.634 106 C1orf135 0.6333 107 PSRC1 0.633 108 VRK1 0.6323 109CKAP2 0.6307 110 CCDC99 0.6303 111 CCNE1 0.6283 112 LMNB2 0.625 113GPSM2 0.625 114 PAICS 0.6243 115 MCAM 0.6227 116 DSN1 0.622 117 NCAPD20.6213 118 RAD54L 0.6213 119 PDSS1 0.6203 120 HN1 0.62 121 C21orf450.6193 122 CTSL2 0.619 123 CTPS 0.6183 124 MCM7 0.618 125 ZWILCH 0.618126 RFC5 0.6177

TABLE 10 Correl. Gene w/CCG Gene # Symbol mean 1 DLGAP5 0.931 2 ASPM0.931 3 KIF11 0.926 4 BIRC5 0.916 5 CDCA8 0.902 6 CDC20 0.9 7 MCM100.899 8 PRC1 0.895 9 BUB1B 0.892 10 FOXM1 0.889 11 NUSAP1 0.888 12C18orf24 0.885 13 PLK1 0.879 14 CDKN3 0.874 15 RRM2 0.871 16 RAD51 0.86417 CEP55 0.862 18 ORC6L 0.86 19 RAD54L 0.86 20 CDC2 0.858 21 CENPF 0.85522 TOP2A 0.852 23 KIF20A 0.851 24 KIAA0101 0.839 25 CDCA3 0.835 26 ASF1B0.797 27 CENPM 0.786 28 TK1 0.783 29 PBK 0.775 30 PTTG1 0.751 31 DTL0.737

TABLE 11 56 CCGs Ranked by Correlation to Mean in Example 5 (“Panel G”)Gene # Gene Symbol Correl. w/CCG mean 1 FOXM1 0.908 2 CDC20 0.907 3CDKN3 0.9 4 CDC2 0.899 5 KIF11 0.898 6 KIAA0101 0.89 7 NUSAP1 0.887 8CENPF 0.882 9 ASPM 0.879 10 BUB1B 0.879 11 RRM2 0.876 12 DLGAP5 0.875 13BIRC5 0.864 14 KIF20A 0.86 15 PLK1 0.86 16 TOP2A 0.851 17 TK1 0.837 18PBK 0.831 19 ASF1B 0.827 20 C18orf24 0.817 21 RAD54L 0.816 22 PTTG10.814 23 KIF4A 0.814 24 CDCA3 0.811 25 MCM10 0.802 26 PRC1 0.79 27 DTL0.788 28 CEP55 0.787 29 RAD51 0.783 30 CENPM 0.781 31 CDCA8 0.774 32OIP5 0.773 33 SHCBP1 0.762 34 ORC6L 0.736 35 CCNB1 0.727 36 CHEK1 0.72337 TACC3 0.722 38 MCM4 0.703 39 FANCI 0.702 40 KIF15 0.701 41 PLK4 0.68842 APOBEC3B 0.67 43 NCAPG 0.667 44 TRIP13 0.653 45 KIF23 0.652 46 NCAPH0.649 47 TYMS 0.648 48 GINS1 0.639 49 STMN1 0.63 50 ZWINT 0.621 51 BLM0.62 52 TTK 0.62 53 CDC6 0.619 54 KIF2C 0.596 55 RAD51AP1 0.567 56NCAPG2 0.535

TABLE 12 15 Housekeeping (HK) Genes Ranked by Correlation to Mean inExample 5 Correaltion Gene with HK Symbol Mean RPL38 0.989 UBA52 0.986PSMC1 0.985 RPL4 0.984 RPL37 0.983 RPS29 0.983 SLC25A3 0.982 CLTC 0.981TXNL1 0.98 PSMA1 0.98 RPL8 0.98 MMADHC 0.979 RPL13A; 0.979 LOC728658PPP2CA 0.978 MRFAP1 0.978

Table 13 below provides a ranking of the CCGs in Panel F according totheir relative predictive value in Example 5.

TABLE 13 Gene # Gene Symbol p-value 1 MCM10 8.60E−10 2 ASPM 2.30E−09 3DLGAP5 1.20E−08 4 CENPF 1.40E−08 5 CDC20 2.10E−08 6 FOXM1 3.40E−07 7TOP2A 4.30E−07 8 NUSAP1 4.70E−07 9 CDKN3 5.50E−07 10 KIF11 6.30E−06 11KIF20A 6.50E−06 12 BUB1B 1.10E−05 13 RAD54L 1.40E−05 14 CEP55 2.60E−0515 CDCA8 3.10E−05 16 TK1 3.30E−05 17 DTL 3.60E−05 18 PRC1 3.90E−05 19PTTG1 4.10E−05 20 CDC2 0.00013 21 ORC6L 0.00017 22 PLK1 0.0005 23C18orf24 0.0011 24 BIRC5 0.00118 25 RRM2 0.00255 26 CENPM 0.0027 27RAD51 0.0028 28 KIAA0101 0.00348 29 CDCA3 0.00863 30 PBK 0.00923 31ASF1B 0.00936

Table 14 below provides a ranking of the CCGs in Panel C according totheir relative predictive value in Example 3.

TABLE 14 Gene p- Gene # Symbol value* 1 NUSAP1 2.8E−07 2 DLG7 5.9E−07 3CDC2 6.0E−07 4 FOXM1 1.1E−06 5 MYBL2 1.1E−06 6 CDCA8 3.3E−06 7 CDC203.8E−06 8 RRM2 7.2E−06 9 PTTG1 1.8E−05 10 CCNB2 5.2E−05 11 HMMR 5.2E−0512 BUB1 8.3E−05 13 PBK 1.2E−04 14 TTK 3.2E−04 15 CDC45L 7.7E−04 16 PRC11.2E−03 17 DTL 1.4E−03 18 CCNB1 1.5E−03 19 TPX2 1.9E−03 20 ZWINT 9.3E−0321 KIF23 1.1E−02 22 TRIP13 1.7E−02 23 KPNA2 2.0E−02 24 UBE2C 2.2E−02 25MELK 2.5E−02 26 CENPA 2.9E−02 27 CKS2 5.7E−02 28 MAD2L1 1.7E−01 29 UBE2S2.0E−01 30 AURKA 4.8E−01 31 TIMELESS 4.8E−01 *p-value for likelihoodratio test of full (post-RP nomogram score + cell cycle expression +nomogram:cell cycle) vs reduced (post-RP nomogram score only) CoxPHmodel of time-torecurrence.

Thus in some embodiments the plurality of test genes comprises at leastsome number of CCGs (e.g., at least 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25,30, 35, 40, 45, 50 or more CCGs) and this plurality of CCGs comprisesthe top 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 35,40 or more CCGs listed in Tables 9-11, & 13-14. In some embodiments theplurality of test genes comprises at least some number of CCGs (e.g., atleast 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50 or moreCCGs) and this plurality of CCGs comprises at least 1, 2, 3, 4, 5, 6, 7,8, 9, 10, 15, or 20 of the following genes: ASPM, BIRC5, BUB1B, CCNB2,CDC2, CDC20, CDCA8, CDKN3, CENPF, DLGAP5, FOXM1, KIAA0101, KIF11, KIF2C,KIF4A, MCM10, NUSAP1, PRC1, RACGAP1, and TPX2. In some embodiments theplurality of test genes comprises at least some number of CCGs (e.g., atleast 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50 or moreCCGs) and this plurality of CCGs comprises any one, two, three, four,five, six, seven, eight, nine, or ten or all of gene numbers 1 & 2, 1 to3, 1 to 4, 1 to 5, 1 to 6, 1 to 7, 1 to 8, 1 to 9, or 1 to 10 of any ofTables 9-11, & 13-14. In some embodiments the plurality of test genescomprises at least some number of CCGs (e.g., at least 3, 4, 5, 6, 7, 8,9, 10, 15, 20, 25, 30, 35, 40, 45, 50 or more CCGs) and this pluralityof CCGs comprises any one, two, three, four, five, six, seven, eight, ornine or all of gene numbers 2 & 3, 2 to 4, 2 to 5, 2 to 6, 2 to 7, 2 to8, 2 to 9, or 2 to 10 of any of Tables 9-11, & 13-14. In someembodiments the plurality of test genes comprises at least some numberof CCGs (e.g., at least 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40,45, 50 or more CCGs) and this plurality of CCGs comprises any one, two,three, four, five, six, seven, or eight or all of gene numbers 3 & 4, 3to 5, 3 to 6, 3 to 7, 3 to 8, 3 to 9, or 3 to 10 of any of Tables 9-11,& 13-14. In some embodiments the plurality of test genes comprises atleast some number of CCGs (e.g., at least 3, 4, 5, 6, 7, 8, 9, 10, 15,20, 25, 30, 35, 40, 45, 50 or more CCGs) and this plurality of CCGscomprises any one, two, three, four, five, six, or seven or all of genenumbers 4 & 5, 4 to 6, 4 to 7, 4 to 8, 4 to 9, or 4 to 10 of any ofTables 9-11, & 13-14. In some embodiments the plurality of test genescomprises at least some number of CCGs (e.g., at least 3, 4, 5, 6, 7, 8,9, 10, 15, 20, 25, 30, 35, 40, 45, 50 or more CCGs) and this pluralityof CCGs comprises any one, two, three, four, five, six, seven, eight,nine, 10, 11, 12, 13, 14, or 15 or all of gene numbers 1 & 2, 1 to 3, 1to 4, 1 to 5, 1 to 6, 1 to 7, 1 to 8, 1 to 9, 1 to 10, 1 to 11, 1 to 12,1 to 13, 1 to 14, or 1 to 15 of any of Tables 9-11, & 13-14.

It has further been discovered that CCG status synergistically adds toclinical parameters in prognosing cancer. In the case of prostatecancer, for example, it has been discovered that a high level of geneexpression of any one of the genes in Panels C through F is associatedwith an increased risk of prostate cancer recurrence or progression inpatients whose clinical nomogram score indicates a relatively low riskof recurrence or progression. Because evaluating CCG expression levelscan thus detect increased risk not detected using clinical parametersalone, the disclosure generally provides methods combining evaluating atleast one clinical parameter with evaluating the status of at least oneCCG.

As Example 3 shows, even individual CCGs add to clinical parameters inpredicting cancer recurrence. Thus one aspect of the disclosure providesan in vitro diagnostic method comprising determining at least oneclinical parameter for a cancer patient and determining the status of atleast one CCG in a sample obtained from the patient. However, assessingthe status of multiple CCGs improves predictive power even more (alsoshown in Example 1). Thus in some embodiments the status of a pluralityof CCGs (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 40, 50 ormore) is determined. In some embodiments abnormal status indicates anincreased likelihood of recurrence or progression. In some embodimentsthe patient has prostate cancer. In some embodiments the patient haslung cancer. Often the clinical parameter is at least somewhatindependently predictive of recurrence or progression and the additionof CCG status improves the predictive power. As used herein, “clinicalparameter” and “clinical measure” refer to disease or patientcharacteristics that are typically applied to assess disease courseand/or predict outcome. Examples in cancer generally include tumorstage, tumor grade, lymph node status, histology, performance status,type of surgery, surgical margins, type of treatment, and age of onset.In prostate cancer clinicians often use pre-surgery blood PSA levels,stage (defined by size of tumor and evidence of metastasis), and Gleasonscore (similar to concept of grade). After surgical intervention,important clinical parameters in prostate cancer include margin andlymph node status. In breast cancer clinicians often use size of indexlesion in cm, invasion, number of nodes involved, and grade.

Often certain clinical parameters are correlated with a particulardisease character. For example, in cancer generally as well as inspecific cancers, certain clinical parameters are correlated with, e.g.,likelihood of recurrence or metastasis, prognosis for survival for acertain amount of time, likelihood of response to treatment generally orto a specific treatment, etc. In prostate cancer some clinicalparameters are such that their status (presence, absence, level, etc.)is associated with increased likelihood of recurrence. Examples of suchrecurrence-associated parameters (some but not all of which are specificto prostate cancer) include high PSA levels (e.g., greater than 4ng/ml), high Gleason score, large tumor size, evidence of metastasis,advanced tumor stage, nuclear grade, lymph node involvement, early ageof onset. Other types of cancer may have different parameters correlatedto likelihood of recurrence or progression, and CCG status, as a measureof proliferative activity, adds to these parameters in predictingprognosis in these cancers. As used herein, “recurrence-associatedclinical parameter” has its conventional meaning for each specificcancer, with which those skilled in the art are quite familiar. In fact,those skilled in the art are familiar with various recurrence-associatedclinical parameters beyond those listed here.

Often a physician will assess more than one clinical parameter in apatient and make a more comprehensive evaluation for the diseasecharacters of interest. Example 5 shows how CCG status can add to oneparticular grouping of clinical parameters used to determine risk ofrecurrence in prostate cancer. Clinical parameters in Example 5 includebinary variables for organ-confined disease and Gleason score less thanor equal to 6, and a continuous variable for logarithmic PSA (Table I).This model includes all of the clinical parameters incorporated in thepost-RP nomogram (i.e., Kattan-Stephenson nomogram) except for Year ofRP and the two components of the Gleason score. Thus in some embodimentsat least two clinical parameters (e.g., two of the above listedparameters) are assessed along with the expression level of at least oneCCG.

One way in which single, but more often multiple, clinical parametersare utilized by physicians is with the help of nomograms. In theclinical setting, nomograms are representations (often visual) of acorrelation between one or more parameters and one or more patient ordisease characters. An example of a prevalent clinical nomogram used indetermining a prostate cancer patient's likelihood of recurrence isdescribed in Kattan et al., J. CLIN. ONCOL. (1999) 17:1499-1507, andupdated in Stephenson et al., J. CLIN. ONCOL. (2005) 23:7005-7012(“Kattan-Stephenson nomogram”). This nomogram evaluates a patient byassigning a point value to each of several clinical parameters (year ofRP, surgical margins, extracapsular extension, seminal vesicle invasion,lymph node involvement, primary Gleason score, secondary Gleason score,and preoperative PSA level), totaling the points for a patient into anomogram score, and then predicting the patient's likelihood of beingrecurrence-free at varying time intervals (up to 10 years) based on thisnomogram score. An example of a prevalent clinical nomogram used indetermining a breast cancer patient's prognosis for survival is theNottingham Prognostic Index (NPI). See, e.g., Galea et al., BREASTCANCER RES. & TREAT. (1992) 22:207-19.

It has been discovered that determining the status of a CCG in a sampleobtained from a prostate cancer patient, along with the patient'sKattan-Stephenson nomogram score, is a better predictor of 10-yearrecurrence-free survival than the nomogram score alone. See, e.g.,Examples 2 & 5, infra. Specifically, adding CCG status to theKattan-Stephenson nomogram detects patients at significantly increasedrisk of recurrence that the nomogram alone does not. Table 7 aboveprovides an exemplary panel of 31 CCGs (Panel C) and a subset panel of26 CCGs (Panel D, shown with *) determined in Example 2 to showpredictive synergy with the Kattan-Stephenson nomogram in prostatecancer prognosis. It has also been discovered that determining thestatus of a CCG in a sample obtained from a breast cancer patient, alongwith the patient's NPI score, is a better prognostic predictor than NPIscore alone. See, e.g., Example 6, infra. Specifically, adding CCGstatus to the NPI nomogram detects patients at significantly increasedrisk of recurrence that the nomogram alone does not. Panels B, C and Dwere determined in Example 2 to show predictive synergy with the NPInomogram in breast cancer prognosis.

Thus another aspect of the disclosure provides an in vitro methodcomprising determining a clinical nomogram score (e.g.,Kattan-Stephenson or NPI nomogram score) for a cancer patient anddetermining the status of at least one CCG in a sample obtained from thepatient. Example 3 illustrates the empirical determination of thepredictive power of individual CCGs and of several CCG panels of varyingsize over the Kattan-Stephenson nomogram. Randomly selected subsets ofthe 31 CCGs listed in Table 7 were tested as distinct CCG signatures andpredictive power (i.e., p-value) was determined for each. As FIG. 1shows, CCG signatures of 2, 3, 4, 5, 6, 10, 15, 20, 25, and 26 geneseach add predictive power to the nomogram. Thus the disclosure providesa method of determining whether a prostate cancer patient has anincreased likelihood of recurrence comprising determining the status ofa panel of genes comprising at least 2, 3, 4, 5, 6, 10, 15, 20, 25, 26,27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 45, 50, 60, 70, 80, 90, or 100or more CCGs, wherein an elevated status (e.g., increased expression)for the CCGs indicates an increased likelihood of recurrence. In someembodiments the method further comprises determining a clinical nomogramscore of the patient. The disclosure further provides a method ofdetermining whether a breast cancer patient has an increased likelihoodof recurrence comprising determining the status of a panel of genescomprising at least 2, 3, 4, 5, 6, 10, 15, 20, 25, 26, 27, 28, 29, 30,31, 32, 33, 34, 35, 40, 45, 50, 60, 70, 80, 90, or 100 or more CCGs,wherein an elevated status (e.g., increased expression) for the CCGsindicates an increased likelihood of recurrence. In some embodiments themethod further comprises determining a clinical nomogram score of thepatient. In some embodiments, the method comprises at least one of thefollowing steps: (a) correlating elevated status (e.g., high orincreased expression) of the panel of genes to an increased likelihoodof recurrence; (b) concluding that the patient has an increasedlikelihood of recurrence based at least in part on elevated status(e.g., high or increased expression) of the panel of genes; or (c)communicating that the patient has an increased likelihood of recurrencebased at least in part on elevated status (e.g., high or increasedexpression) of the panel of genes.

Often clinical nomograms for cancer are designed such that a particularvalue (e.g., high score) correlates with an increased risk ofrecurrence. Elevated CCG status (e.g., increased expression or activity)is also correlated with increased risk. Thus, in some embodiments thedisclosure provides a method of determining whether a cancer patient hasan increased likelihood of recurrence or progression comprisingdetermining a clinical nomogram score for the patient and determiningthe status of at least one CCG in a sample obtained from the patient,wherein a high nomogram score and/or an elevated CCG status indicate thepatient has an increased likelihood of recurrence or progression. Insome embodiments the cancer is prostate cancer. In some embodiments thecancer is lung cancer. In some embodiments, the method comprises atleast one of the following steps: (a) correlating a high nomogram scoreand/or an elevated CCG status (e.g., high or increased expression) to anincreased likelihood of recurrence or progression; (b) concluding thatthe patient has an increased likelihood of recurrence or progressionbased at least in part on a high nomogram score and/or an elevated CCGstatus (e.g., high or increased expression); or (c) communicating thatthe patient has an increased likelihood of recurrence or progressionbased at least in part on a high nomogram score and/or an elevated CCGstatus (e.g., high or increased expression).

In some embodiments this assessment is made before radical prostatectomy(e.g., using a prostate biopsy sample) while in some embodiments it ismade after (e.g., using the resected prostate sample). In someembodiments, a sample of one or more cells are obtained from a prostatecancer patient before or after treatment for analysis according to thepresent disclosure. Prostate cancer treatment currently applied in theart includes, e.g., prostatectomy, radiotherapy, hormonal therapy (e.g.,using GnRH antagonists, GnRH agonists, antiandrogens), chemotherapy, andhigh intensity focused ultrasound. In some embodiments, one or moreprostate tumor cells from prostate cancer tissue are obtained from aprostate cancer patient during biopsy or prostatectomy and are used foranalysis in the method of the present disclosure.

The present disclosure is also based on the discovery that PTEN statuspredicts aggressive prostate cancer. PTEN status adds to both clinicalparameters (e.g., Kattan-Stephenson nomogram) and CCGs (e.g., the genesin Table 1 or Panels A through G). As described in more detail inExample 4 below, PTEN status was determined in 191 prostate cancerpatient samples with accompanying clinical history data and CCGsignature data. Negative PTEN status was found to be a significantpredictor for risk of recurrence (p-value 0.031). PTEN remained asignificant predictor of recurrence after adjusting for post-surgeryclinical parameters and the CCG signature shown in Table 7 (p-value0.026). In addition, and importantly, the combination of PTEN and theCCG signature seems to be a better predictor of recurrence thanpost-surgery clinical parameters (p-value 0.0002).

Because PTEN is an independent predictor of prostate cancer recurrence,one aspect of the disclosure provides a method of predicting a patient'slikelihood of prostate cancer recurrence comprising determining PTENstatus in a sample from the patient, wherein a low or negative PTENstatus indicates the patient has an increased likelihood of recurrence.In some embodiments, the method comprises at least one of the followingsteps: (a) correlating low or negative PTEN status (e.g., low ornegative expression) to an increased likelihood of recurrence; (b)concluding that the patient has an increased likelihood of recurrencebased at least in part on low or negative PTEN status (e.g., low ornegative expression); or (c) communicating that the patient has anincreased likelihood of recurrence based at least in part on low ornegative PTEN status (e.g., low or negative expression). PTEN status canbe determined by any technique known in the art, including but notlimited to those discussed herein.

Because PTEN adds to CCG status in predicting prostate cancerrecurrence, another aspect of the disclosure provides an in vitro methodcomprising determining PTEN status and determining the status of aplurality of CCGs in a sample obtained from a patient. Differentcombinations of techniques can be used to determine the status thevarious markers. For example, in one embodiment PTEN status isdetermined by immunohistochemistry (IHC) while the status of theplurality of CCGs is determined by quantitative polymerase chainreaction (qPCR™), e.g., TaqMan™. Some embodiments of the disclosureprovide a method of determining a prostate cancer patient's likelihoodof recurrence comprising determining PTEN status in a sample obtainedfrom the patient, determining the status of a plurality of CCGs in asample obtained from the patient, wherein low or negative PTEN statusand/or elevated CCG status indicate the patient has an increasedlikelihood of recurrence. In some embodiments, the method comprises atleast one of the following steps: (a) correlating low or negative PTENstatus (e.g., low or negative expression) and/or elevated CCG status(e.g., high or increased expression) to an increased likelihood ofrecurrence; (b) concluding that the patient has an increased likelihoodof recurrence based at least in part on low or negative PTEN status(e.g., low or negative expression) and/or elevated CCG status (e.g.,high or increased expression); or (c) communicating that the patient hasan increased likelihood of recurrence based at least in part on low ornegative PTEN status (e.g., low or negative expression) and/or elevatedCCG status (e.g., high or increased expression).

Because PTEN status adds predictive value to clinical parameters inpredicting prostate recurrence, yet another aspect of the disclosureprovides an in vitro method comprising determining PTEN status anddetermining at least one clinical parameter for a cancer patient. Oftenthe clinical parameter is at least somewhat independently predictive ofrecurrence and the addition of PTEN status improves the predictivepower. In some embodiments the disclosure provides a method ofdetermining whether a cancer patient has an increased likelihood ofrecurrence comprising determining the status of PTEN in a sampleobtained from the patient and determining a clinical nomogram score forthe patient, wherein low or negative PTEN status and/or a unfavorable(e.g., high) nomogram score indicate the patient has an increasedlikelihood of recurrence. In some embodiments, the method comprises atleast one of the following steps: (a) correlating low or negative PTENstatus (e.g., low or negative expression) and/or unfavorable (e.g.,high) nomogram score to an increased likelihood of recurrence; (b)concluding that the patient has an increased likelihood of recurrencebased at least in part on low or negative PTEN status (e.g., low ornegative expression) and/or unfavorable (e.g., high) nomogram score; or(c) communicating that the patient has an increased likelihood ofrecurrence based at least in part on low or negative PTEN status (e.g.,low or negative expression) and/or unfavorable (e.g., high) nomogramscore.

Because all three of the above markers are additive, some embodiments ofthe disclosure provide a method of determining whether a cancer patienthas an increased likelihood of recurrence comprising determining thestatus of PTEN in a sample obtained from the patient, determining aclinical nomogram score for the patient and determining the status of atleast one CCG in a sample obtained from the patient, wherein low ornegative PTEN status, an unfavorable (e.g., high) nomogram score and/oran elevated CCG status indicate the patient has an increased likelihoodof recurrence. In some embodiments, the method comprises at least one ofthe following steps: (a) correlating low or negative PTEN status (e.g.,low or negative expression), an unfavorable (e.g., high) nomogram scoreand/or elevated CCG status (e.g., high or increased expression) to anincreased likelihood of recurrence; (b) concluding that the patient hasan increased likelihood of recurrence based at least in part on low ornegative PTEN status (e.g., low or negative expression), an unfavorable(e.g., high) nomogram score and/or elevated CCG status (e.g., high orincreased expression); or (c) communicating that the patient has anincreased likelihood of recurrence based at least in part on low ornegative PTEN status (e.g., low or negative expression), an unfavorable(e.g., high) nomogram score and/or elevated CCG status (e.g., high orincreased expression).

The present disclosure is also based on the discovery thatkallikrein-related peptidase 3 (KLK3) RNA status predicts aggressiveprostate cancer. KLK3 (Entrez Gene Id No. 354) is the gene encoding PSAprotein. KLK3 status adds to both clinical parameters (e.g.,Kattan-Stephenson nomogram) and CCGs (e.g., the genes in Table 1 orPanels A through G). As described in more detail in Examples 7 & 9below, KLK3 RNA expression was measured in prostate cancer patientsamples with accompanying clinical history data and CCG signature data.Of note, KLK3 RNA expression in FFPE was not well-correlated to serumPSA protein levels. Decreased KLK3 expression was found to be asignificant predictor for risk of recurrence (p-value<0.0005). KLK3 wasa significant predictor of recurrence independent of post-surgeryclinical parameters (e.g., Gleason score, PSA) and the CCG signatureshown in Panel F (p-value 2×10⁻⁶).

PCA3 (Entrez Gene Id. No. 50652) is located at 9q21 and has been foundto be androgen sensitive. Genes such as PCA3 that are involved inandrogen signaling have been found to be responsive to androgen receptor(AR). AR signaling promotes cell growth and proliferation in theprostate. Studies have shown that most early prostate cancer is androgendependent (hormone sensitive) and many treatments for early prostatecancer are directed to this characteristic. In particular, certainchemotherapy drugs are directed to this androgen dependency. Forexample, finasteride (dutasteride) blocks conversion of testosterone todihydrotestosterone; LHRH analogs inhibits testicular testosterone,abiraterone inhibits testosterone from testicles, adrena, gland, andprostate; and enzalutamide acts as an AR antagonist. Eventually, overtime, most metastatic prostate cancers eventually become androgenindependent (castration resistant).

The present disclosure is also based on the discovery that RNA status ofPCA3 (prostate cancer associated 3) has prognostic utility in prostatecancer. PCA3 status can add to the prognostic power of CCP scores andcaptures information that is not fully captured by CCP score alone. PCA3status can add to the prognostic power of both clinical parameters andCCP score. As described in more detail in Example 10 below, PCA3 RNAexpression was measured in prostate cancer samples and analyzed alongwith CCP score and clinical history. The analysis of PCA3 expression inlight of clinical data and CCP score revealed that PCA3 status isprognostic of prostate cancer and that inclusion of PCA3 status with CCPscore (as determined by CCGs, e.g., the genes in Table 1 or Panels Athrough G) can increase prognostic power. It is likely that other ARsignaling genes or AR sensitive genes will also be prognostic ofprostate cancer.

Other genes were analyzed specifically for their ability to addprognostic power beyond CCP score and clinical variables. These genesare found in Tables R, S & Y below and form Panels H & I of thedisclosure. Each of these genes can independently be used to diagnose apatient's prognosis for cancer recurrence or cancer-specific deathaccording to the methods, systems, kits, etc. of the disclosurediscussed herein. Or one or more of these genes can be added to a panelof the disclosure comprising CCP genes to form a larger panel withimproved predictive power.

Because KLK3, PCA3 and the genes of Panel H or I are independentpredictors of cancer recurrence and cancer-specific death, one aspect ofthe disclosure provides a method of predicting a patient's prognosis(e.g., likelihood of prostate cancer recurrence or cancer-specificdeath) comprising determining KLK3 status, PCA3 status and/or the statusof one or more genes in Panel H or I in a sample from the patient,wherein an abnormal status (e.g., decreased expression, increasedexpression) indicates the patient has a poor prognosis (e.g., highlikelihood of recurrence or cancer-specific death). In some embodiments,the method comprises at least one of the following steps: (a)correlating abnormal status (e.g., decreased mRNA expression) to a poorprognosis (e.g., high likelihood of recurrence or cancer-specificdeath); (b) concluding that the patient has a poor prognosis (e.g., highlikelihood of recurrence or cancer-specific death) based at least inpart abnormal status (e.g., decreased mRNA expression); or (c)communicating that the patient has a poor prognosis (e.g., highlikelihood of recurrence or cancer-specific death) based at least inpart on abnormal status (e.g., decreased mRNA expression). KLK3 status,PCA3 status, or the status of one or more genes in Panel H or I can bedetermined by applying and adapting techniques known in the art,including but not limited to those discussed herein. In someembodiments, RNA expression is measured, e.g., by directly measuring RNAlevels or by measuring levels of cDNA derived from RNA.

Because KLK3, PCA3 and each of the genes in Panel H or I adds to CCGstatus in predicting cancer recurrence and cancer-specific death,another aspect of the disclosure provides an in vitro method comprisingdetermining KLK3 status, PCA3 status and/or the status of one or moregenes in Panel H or I and determining the status of a plurality of CCGsin a sample obtained from a patient. Some embodiments of the disclosureprovide a method of determining a prostate cancer patient's prognosiscomprising determining KLK3 expression, PCA3 expression and/or theexpression of one or more genes in Panel H or I in a sample obtainedfrom the patient, determining the expression of a plurality of CCGs in asample obtained from the patient, wherein abnormal KLK3 status (e.g.,decreased mRNA expression), abnormal PCA3 status and/or abnormal statusof one or more genes in Panel H or I (e.g., increased mRNA expression)and/or elevated CCG status indicate the patient has a poor prognosis. Insome embodiments, the method comprises at least one of the followingsteps: (a) correlating abnormal KLK3 status (e.g., decreased mRNAexpression), abnormal PCA3 status and/or abnormal status of one or moregenes in Panel H or I and/or elevated CCG status (e.g., high orincreased expression) to a poor prognosis (e.g., high likelihood ofrecurrence or cancer-specific death); (b) concluding that the patienthas a poor prognosis (e.g., high likelihood of recurrence orcancer-specific death) based at least in part on a abnormal KLK3 status(e.g., decreased mRNA expression), abnormal PCA3 status and/or abnormalstatus of one or more genes in Panel H or I and/or elevated CCG status(e.g., high or increased expression); or (c) communicating that thepatient has a poor prognosis (e.g., high likelihood of recurrence orcancer-specific death) based at least in part on abnormal KLK3 status(e.g., decreased mRNA expression), abnormal PCA3 status and/or abnormalstatus of one or more genes in Panel H or I and/or elevated CCG status(e.g., high or increased expression).

Because KLK3 status, PCA3 status and each of the genes in Panel H or Iadds predictive value to clinical parameters in predicting prostaterecurrence, yet another aspect of the disclosure provides an in vitromethod comprising determining KLK3 status, PCA3 status and/or the statusof one or more genes in Panel H or I and determining at least oneclinical parameter for a cancer patient. Often the clinical parameter isat least somewhat independently predictive of recurrence and theaddition of KLK3 status, PCA3 status and/or the status of one or moregenes in Panel H or I improves the predictive power. In some embodimentsthe disclosure provides a method of predicting a patient's prognosis(e.g., likelihood of prostate cancer recurrence or cancer-specificdeath) comprising determining KLK3 expression in a sample obtained fromthe patient, determining PCA3 expression in a sample obtained from thepatient, and/or the status of one or more genes in Panel H or I anddetermining a clinical score for the patient, wherein abnormal KLK3status (e.g., decreased mRNA expression), abnormal PCA3 status and/orabnormal status of one or more genes in Panel H or I and/or anunfavorable (e.g., high) score indicate the patient has a poor prognosis(e.g., increased likelihood of prostate cancer recurrence orcancer-specific death). In some embodiments, the method comprises atleast one of the following steps: (a) correlating abnormal KLK3 status(e.g., decreased mRNA expression), abnormal PCA3 status and/or abnormalstatus of one or more genes in Panel H or I and/or unfavorable (e.g.,high) clinical score to a poor prognosis (e.g., high likelihood ofrecurrence or cancer-specific death); (b) concluding that the patienthas a poor prognosis (e.g., high likelihood of recurrence orcancer-specific death) based at least in part on abnormal KLK3 status(e.g., decreased mRNA expression), abnormal PCA3 status, and/or abnormalstatus of one or more genes in Panel H or I and/or unfavorable (e.g.,high) clinical score; or (c) communicating that the patient has a poorprognosis (e.g., high likelihood of recurrence or cancer-specific death)based at least in part on abnormal KLK3 status (e.g., decreased mRNAexpression), abnormal PCA3 status, and/or abnormal status of one or moregenes in Panel H or I and/or unfavorable (e.g., high) clinical score.

Because all four of the above markers are additive, some embodiments ofthe disclosure provide a method of predicting a patient's prognosis(e.g., likelihood of prostate cancer recurrence or cancer-specificdeath) comprising determining the status of PTEN in a sample obtainedfrom the patient, determining KLK3 expression in a sample obtained fromthe patient, determining a clinical nomogram score for the patient, anddetermining the status of a plurality of CCGs (e.g., Panel F) in asample obtained from the patient, wherein any of (1) low or negativePTEN status, (2) abnormal KLK3 status (e.g., decreased mRNA expression),(3) an unfavorable (e.g., high) nomogram score and/or (4) an elevatedCCG status indicate the patient has a poor prognosis (e.g., increasedlikelihood of prostate cancer recurrence or cancer-specific death). Insome embodiments, the method comprises at least one of the followingsteps: (a) correlating low or negative PTEN status, abnormal KLK3 status(e.g., decreased mRNA expression), abnormal PCA3 status, an unfavorable(e.g., high) nomogram score and/or an elevated CCG status to a poorprognosis (e.g., high likelihood of recurrence or cancer-specificdeath); (b) concluding that the patient has a poor prognosis (e.g., highlikelihood of recurrence or cancer-specific death) based at least inpart on low or negative PTEN status, abnormal KLK3 status (e.g.,decreased mRNA expression), abnormal PCA3 status, an unfavorable (e.g.,high) nomogram score and/or an elevated CCG status; or (c) communicatingthat the patient has a poor prognosis (e.g., high likelihood ofrecurrence or cancer-specific death) based at least in part on low ornegative PTEN status, abnormal KLK3 status (e.g., decreased mRNAexpression), abnormal PCA3 status, an unfavorable (e.g., high) nomogramscore and/or an elevated CCG status. Determining the status of one ormore genes in Panel H or I can also be added to any of these analyses,with abnormal status (e.g., high expression) indicating poor prognosis.

The genes in Tables R, S & Y are ranked according to their p-value(e.g., after adjusting for CCP score). Thus, the various aspects of thedisclosure involving these genes (e.g., the preceding severalparagraphs) may incorporate these genes according this ranking. In someembodiments the plurality of test genes comprises at least some numberof genes from any of Tables R, S or Y (e.g., at least 3, 4, 5, 6, 7, 8,9, 10, 15, 20, 25, 30, 35 or more) and this plurality of genes comprisesthe top 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 35or more genes listed in Table Y. In some embodiments the plurality oftest genes comprises at least some number of genes from any of Tables R,S or Y (e.g., at least 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35 ormore) and this plurality of genes comprises any one, two, three, four,five, six, seven, eight, nine, or ten or all of gene numbers 1 & 2, 1 to3, 1 to 4, 1 to 5, 1 to 6, 1 to 7, 1 to 8, 1 to 9, or 1 to 10 from anyof Tables R, S or Y. In some embodiments the plurality of test genescomprises at least some number of genes from any of Tables R, S or Y(e.g., at least 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35 or more) andthis plurality of genes comprises any one, two, three, four, five, six,seven, eight, or nine or all of gene numbers 2 & 3, 2 to 4, 2 to 5, 2 to6, 2 to 7, 2 to 8, 2 to 9, or 2 to 10 from any of Tables R, S or Y. Insome embodiments the plurality of test genes comprises at least somenumber of genes from any of Tables R, S or Y (e.g., at least 3, 4, 5, 6,7, 8, 9, 10, 15, 20, 25, 30, 35 or more) and this plurality of genescomprises any one, two, three, four, five, six, seven, or eight or allof gene numbers 3 & 4, 3 to 5, 3 to 6, 3 to 7, 3 to 8, 3 to 9, or 3 to10 from any of Tables R, S or Y. In some embodiments the plurality oftest genes comprises at least some number of genes from any of Tables R,S or Y (e.g., at least 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35 ormore) and this plurality of genes comprises any one, two, three, four,five, six, or seven or all of gene numbers 4 & 5, 4 to 6, 4 to 7, 4 to8, 4 to 9, or 4 to 10 from any of Tables R, S or Y. In some embodimentsthe plurality of test genes comprises at least some number of genes fromany of Tables R, S or Y (e.g., at least 3, 4, 5, 6, 7, 8, 9, 10, 15, 20,25, 30, 35 or more) and this plurality of genes comprises any one, two,three, four, five, six, seven, eight, nine, 10, 11, 12, 13, 14, or 15 orall of gene numbers 1 & 2, 1 to 3, 1 to 4, 1 to 5, 1 to 6, 1 to 7, 1 to8, 1 to 9, 1 to 10, 1 to 11, 1 to 12, 1 to 13, 1 to 14, or 1 to 15 fromany of Tables R, S or Y.

The results of any analyses according to the disclosure will often becommunicated to physicians, genetic counselors and/or patients (or otherinterested parties such as researchers) in a transmittable form that canbe communicated or transmitted to any of the above parties. Such a formcan vary and can be tangible or intangible. The results can be embodiedin descriptive statements, diagrams, photographs, charts, images or anyother visual forms. For example, graphs showing expression or activitylevel or sequence variation information for various genes can be used inexplaining the results. Diagrams showing such information for additionaltarget gene(s) are also useful in indicating some testing results. Thestatements and visual forms can be recorded on a tangible medium such aspapers, computer readable media such as floppy disks, compact disks,etc., or on an intangible medium, e.g., an electronic medium in the formof email or website on internet or intranet. In addition, results canalso be recorded in a sound form and transmitted through any suitablemedium, e.g., analog or digital cable lines, fiber optic cables, etc.,via telephone, facsimile, wireless mobile phone, internet phone and thelike.

Thus, the information and data on a test result can be produced anywherein the world and transmitted to a different location. As an illustrativeexample, when an expression level, activity level, or sequencing (orgenotyping) assay is conducted outside the United States, theinformation and data on a test result may be generated, cast in atransmittable form as described above, and then imported into the UnitedStates. Accordingly, the present disclosure also encompasses a methodfor producing a transmittable form of information on at least one of (a)expression level or (b) activity level for at least one patient sample.The method comprises the steps of (1) determining at least one of (a) or(b) above according to methods of the present disclosure; and (2)embodying the result of the determining step in a transmittable form.The transmittable form is the product of such a method.

Techniques for analyzing such expression, activity, and/or sequence data(indeed any data obtained according to the disclosure) will often beimplemented using hardware, software or a combination thereof in one ormore computer systems or other processing systems capable ofeffectuating such analysis.

Thus, the present disclosure further provides a system for determininggene expression in a tumor sample, comprising: (1) a sample analyzer fordetermining the expression levels of a panel of genes in a tumor sampleincluding at least 2, 4, 6, 8 or 10 cell-cycle genes, wherein the sampleanalyzer contains the tumor sample which is from a patient identified ashaving prostate cancer, lung cancer, bladder cancer or brain cancer, orcDNA molecules from mRNA expressed from the panel of genes; (2) a firstcomputer program for (a) receiving gene expression data on at least 4test genes selected from the panel of genes, (b) weighting thedetermined expression of each of the test genes, and (c) combining theweighted expression to provide a test value, wherein at least 20%, 50%,at least 75% or at least 90% of the test genes are cell-cycle genes; andoptionally (3) a second computer program for comparing the test value toone or more reference values each associated with a predetermined degreeof risk of cancer recurrence or progression of the prostate cancer, lungcancer, bladder cancer or brain cancer. In some embodiments, the systemfurther comprises a display module displaying the comparison between thetest value to the one or more reference values, or displaying a resultof the comparing step.

In preferred embodiment, the amount of RNA transcribed from the panel ofgenes including test genes is measured in the tumor sample. In addition,the amount of RNA of one or more housekeeping genes in the tumor sampleis also measured, and used to normalize or calibrate the expression ofthe test genes, as described above.

In some embodiments, the plurality of test genes includes at least 2, 3or 4 cell-cycle genes, which constitute at least 50%, 75% or 80% of theplurality of test genes, and preferably 100% of the plurality of testgenes. In some embodiments, the plurality of test genes includes atleast 5, 6 or 7, or at least 8 cell-cycle genes, which constitute atleast 20%, 25%, 30%, 40%, 50%, 60%, 70%, 75%, 80% or 90% of theplurality of test genes, and preferably 100% of the plurality of testgenes.

In some other embodiments, the plurality of test genes includes at least8, 10, 12, 15, 20, 25 or 30 cell-cycle genes, which constitute at least20%, 25%, 30%, 40%, 50%, 60%, 70%, 75%, 80% or 90% of the plurality oftest genes, and preferably 100% of the plurality of test genes.

The sample analyzer can be any instruments useful in determining geneexpression, including, e.g., a sequencing machine, a real-time PCRmachine, and a microarray instrument.

The computer-based analysis function can be implemented in any suitablelanguage and/or browsers. For example, it may be implemented with Clanguage and preferably using object-oriented high-level programminglanguages such as Visual Basic, SmallTalk, C++, and the like. Theapplication can be written to suit environments such as the MicrosoftWindows™ environment including Windows™ 98, Windows™ 2000, Windows™ NT,and the like. In addition, the application can also be written for theMacIntosh™, SUN™, UNIX or LINUX environment. In addition, the functionalsteps can also be implemented using a universal or platform-independentprogramming language. Examples of such multi-platform programminglanguages include, but are not limited to, hypertext markup language(HTML), JAVA™, JavaScript™, Flash programming language, common gatewayinterface/structured query language (CGI/SQL), practical extractionreport language (PERL), AppleScript™ and other system script languages,programming language/structured query language (PL/SQL), and the like.Java™- or JavaScript™-enabled browsers such as HotJava™, Microsoft™Explorer™, or Netscape™ can be used. When active content web pages areused, they may include Java™ applets or ActiveX™ controls or otheractive content technologies.

The analysis function can also be embodied in computer program productsand used in the systems described above or other computer- orinternet-based systems. Accordingly, another aspect of the presentdisclosure relates to a computer program product comprising acomputer-usable medium having computer-readable program codes orinstructions embodied thereon for enabling a processor to carry out genestatus analysis. These computer program instructions may be loaded ontoa computer or other programmable apparatus to produce a machine, suchthat the instructions which execute on the computer or otherprogrammable apparatus create means for implementing the functions orsteps described above. These computer program instructions may also bestored in a computer-readable memory or medium that can direct acomputer or other programmable apparatus to function in a particularmanner, such that the instructions stored in the computer-readablememory or medium produce an article of manufacture includinginstructions which implement the analysis. The computer programinstructions may also be loaded onto a computer or other programmableapparatus to cause a series of operational steps to be performed on thecomputer or other programmable apparatus to produce a computerimplemented process such that the instructions which execute on thecomputer or other programmable apparatus provide steps for implementingthe functions or steps described above.

Thus one aspect of the present disclosure provides a system fordetermining whether a patient has increased likelihood of recurrence.Generally speaking, the system comprises (1) computer program forreceiving, storing, and/or retrieving a patient's gene status data(e.g., expression level, activity level, variants) and optionallyclinical parameter data (e.g., Gleason score, nomogram score); (2)computer program for querying this patient data; (3) computer programfor concluding whether there is an increased likelihood of recurrencebased on this patient data; and optionally (4) computer program foroutputting/displaying this conclusion. In some embodiments this computerprogram for outputting the conclusion may comprise a computer programfor informing a health care professional of the conclusion.

One example of such a computer system is the computer system [600]illustrated in FIG. 6. Computer system [600] may include at least oneinput module [630] for entering patient data into the computer system[600]. The computer system [600] may include at least one output module[624] for indicating whether a patient has an increased or decreasedlikelihood of response and/or indicating suggested treatments determinedby the computer system [600]. Computer system [600] may include at leastone memory module [606] in communication with the at least one inputmodule [630] and the at least one output module [624].

The at least one memory module [606] may include, e.g., a removablestorage drive [608], which can be in various forms, including but notlimited to, a magnetic tape drive, a floppy disk drive, a VCD drive, aDVD drive, an optical disk drive, etc. The removable storage drive [608]may be compatible with a removable storage unit [610] such that it canread from and/or write to the removable storage unit [610]. Removablestorage unit [610] may include a computer usable storage medium havingstored therein computer-readable program codes or instructions and/orcomputer readable data. For example, removable storage unit [610] maystore patient data. Example of removable storage unit [610] are wellknown in the art, including, but not limited to, floppy disks, magnetictapes, optical disks, and the like. The at least one memory module [606]may also include a hard disk drive [612], which can be used to storecomputer readable program codes or instructions, and/or computerreadable data.

In addition, as shown in FIG. 1, the at least one memory module [606]may further include an interface [614] and a removable storage unit[616] that is compatible with interface [614] such that software,computer readable codes or instructions can be transferred from theremovable storage unit [616] into computer system [600]. Examples ofinterface [614] and removable storage unit [616] pairs include, e.g.,removable memory chips (e.g., EPROMs or PROMs) and sockets associatedtherewith, program cartridges and cartridge interface, and the like.Computer system [600] may also include a secondary memory module [618],such as random access memory (RAM).

Computer system [600] may include at least one processor module [602].It should be understood that the at least one processor module [602] mayconsist of any number of devices. The at least one processor module[602] may include a data processing device, such as a microprocessor ormicrocontroller or a central processing unit. The at least one processormodule

may include another logic device such as a DMA (Direct Memory Access)processor, an integrated communication processor device, a custom VLSI(Very Large Scale Integration) device or an ASIC (Application SpecificIntegrated Circuit) device. In addition, the at least one processormodule [602] may include any other type of analog or digital circuitrythat is designed to perform the processing functions described herein.

As shown in FIG. 6, in computer system [600], the at least one memorymodule [606], the at least one processor module [602], and secondarymemory module [618] are all operably linked together throughcommunication infrastructure [620], which may be a communications bus,system board, cross-bar, etc.). Through the communication infrastructure[620], computer program codes or instructions or computer readable datacan be transferred and exchanged. Input interface [626] may operablyconnect the at least one input module [626] to the communicationinfrastructure [620]. Likewise, output interface [622] may operablyconnect the at least one output module [624] to the communicationinfrastructure [620].

The at least one input module [630] may include, for example, akeyboard, mouse, touch screen, scanner, and other input devices known inthe art. The at least one output module [624] may include, for example,a display screen, such as a computer monitor, TV monitor, or the touchscreen of the at least one input module [630]; a printer; and audiospeakers. Computer system [600] may also include, modems, communicationports, network cards such as Ethernet cards, and newly developed devicesfor accessing intranets or the internet.

The at least one memory module [606] may be configured for storingpatient data entered via the at least one input module [630] andprocessed via the at least one processor module [602]. Patient datarelevant to the present disclosure may include expression level,activity level, copy number and/or sequence information for PTEN and/ora CCG. Patient data relevant to the present disclosure may also includeclinical parameters relevant to the patient's disease. Any other patientdata a physician might find useful in making treatmentdecisions/recommendations may also be entered into the system, includingbut not limited to age, gender, and race/ethnicity and lifestyle datasuch as diet information. Other possible types of patient data includesymptoms currently or previously experienced, patient's history ofillnesses, medications, and medical procedures.

The at least one memory module [606] may include a computer-implementedmethod stored therein. The at least one processor module [602] may beused to execute software or computer-readable instruction codes of thecomputer-implemented method. The computer-implemented method may beconfigured to, based upon the patient data, indicate whether the patienthas an increased likelihood of recurrence, progression or response toany particular treatment, generate a list of possible treatments, etc.

In certain embodiments, the computer-implemented method may beconfigured to identify a patient as having or not having an increasedlikelihood of recurrence or progression. For example, thecomputer-implemented method may be configured to inform a physician thata particular patient has an increased likelihood of recurrence.Alternatively or additionally, the computer-implemented method may beconfigured to actually suggest a particular course of treatment based onthe answers to/results for various queries.

FIG. 7 illustrates one embodiment of a computer-implemented method [700]of the disclosure that may be implemented with the computer system [600]of the disclosure. The method [700] begins with one of three queries([710], [711], [712]), either sequentially or substantiallysimultaneously. If the answer to/result for any of these queries is“Yes” [720], the method concludes [730] that the patient has anincreased likelihood of recurrence. If the answer to/result for all ofthese queries is “No” [721], the method concludes [731] that the patientdoes not have an increased likelihood of recurrence. The method [700]may then proceed with more queries, make a particular treatmentrecommendation ([740], [741]), or simply end.

When the queries are performed sequentially, they may be made in theorder suggested by FIG. 7 or in any other order. Whether subsequentqueries are made can also be dependent on the results/answers forpreceding queries. In some embodiments of the method illustrated in FIG.7, for example, the method asks about clinical parameters [712] firstand, if the patient has one or more clinical parameters identifying thepatient as at increased risk for recurrence then the method concludessuch [730] or optionally confirms by querying CCG status, while if thepatient has no such clinical parameters then the method proceeds to askabout CCG status [711]. Optionally, if CCG status is not elevated, thenthe method may continue to ask about PTEN status [710]. As mentionedabove, the preceding order of queries may be modified. In someembodiments an answer of “yes” to one query (e.g., [712]) prompts one ormore of the remaining queries to confirm that the patient has increasedrisk of recurrence.

In some embodiments, the computer-implemented method of the disclosure[700] is open-ended. In other words, the apparent first step [710, 711,and/or 712] in FIG. 7 may actually form part of a larger process and,within this larger process, need not be the first step/query. Additionalsteps may also be added onto the core methods discussed above. Theseadditional steps include, but are not limited to, informing a healthcare professional (or the patient itself) of the conclusion reached;combining the conclusion reached by the illustrated method [700] withother facts or conclusions to reach some additional or refinedconclusion regarding the patient's diagnosis, prognosis, treatment,etc.; making a recommendation for treatment (e.g., “patientshould/should not undergo radical prostatectomy”); additional queriesabout additional biomarkers, clinical parameters, or other usefulpatient information (e.g., age at diagnosis, general patient health,etc.).

Regarding the above computer-implemented method [700], the answers tothe queries may be determined by the method instituting a search ofpatient data for the answer. For example, to answer the respectivequeries [710, 711, 712], patient data may be searched for PTEN status(e.g., PTEN IHC or mutation screening), CCG status (e.g., CCG expressionlevel data), or clinical parameters (e.g., Gleason score, nomogramscore, etc.). If such a comparison has not already been performed, themethod may compare these data to some reference in order to determine ifthe patient has an abnormal (e.g., elevated, low, negative) status.Additionally or alternatively, the method may present one or more of thequeries [710, 711, 712] to a user (e.g., a physician) of the computersystem [100]. For example, the questions [710, 711, 712] may bepresented via an output module [624]. The user may then answer “Yes” or“No” via an input module [630]. The method may then proceed based uponthe answer received. Likewise, the conclusions [730, 731] may bepresented to a user of the computer-implemented method via an outputmodule [624].

Thus in some embodiments the disclosure provides a method comprising:accessing information on a patient's CCG status, clinical parametersand/or PTEN status stored in a computer-readable medium; querying thisinformation to determine at least one of whether a sample obtained fromthe patient shows increased expression of at least one CCG whether thepatient has a recurrence-associated clinical parameter, and/or whetherthe patient has a low/negative PTEN status, outputting [or displaying]the sample's CCG expression status, the patient's recurrence-associatedclinical parameter status, and/or the sample's PTEN status. As usedherein in the context of computer-implemented embodiments of thedisclosure, “displaying” means communicating any information by anysensory manner. Examples include, but are not limited to, visualdisplays, e.g., on a computer screen or on a sheet of paper printed atthe command of the computer, and auditory displays, e.g., computergenerated or recorded auditory expression of a patient's genotype.

As discussed at length above, recurrence-associated clinical parametersor PTEN status combined with elevated CCG status indicate asignificantly increased likelihood of recurrence. Thus some embodimentsprovide a computer-implemented method of determining whether a patienthas an increased likelihood of recurrence comprising accessinginformation on a patient's PTEN status (e.g., from a tumor sampleobtained from the patient) or clinical parameters and CCG status (e.g.,from a tumor sample obtained from the patient) stored in acomputer-readable medium; querying this information to determine atleast one of whether the patient has a low/negative PTEN status orwhether the patient has a recurrence-associated clinical parameter;querying this information to determine whether a sample obtained fromthe patient shows increased expression of at least one CCG; outputting(or displaying) an indication that the patient has an increasedlikelihood of recurrence if the patient has a low/negative PTEN statusor a recurrence-associated clinical parameter and the sample showsincreased expression of at least one CCG Some embodiments furthercomprise displaying PTEN, clinical parameters (or their values) and/orthe CCGs and their status (including, e.g., expression levels),optionally together with an indication of whether the PTEN or CCG statusand/or clinical parameter indicates increased likelihood of risk.

The practice of the present disclosure may also employ conventionalbiology methods, software and systems. Computer software products of thedisclosure typically include computer readable media havingcomputer-executable instructions for performing the logic steps of themethod of the disclosure. Suitable computer readable medium includefloppy disk, CD-ROM/DVD/DVD-ROM, hard-disk drive, flash memory, ROM/RAM,magnetic tapes and etc. Basic computational biology methods aredescribed in, for example, Setubal et al., INTRODUCTION TO COMPUTATIONALBIOLOGY METHODS (PWS Publishing Company, Boston, 1997); Salzberg et al.(Ed.), COMPUTATIONAL METHODS IN MOLECULAR BIOLOGY, (Elsevier, Amsterdam,1998); Rashidi & Buehler, BIOINFORMATICS BASICS: APPLICATION INBIOLOGICAL SCIENCE AND MEDICINE (CRC Press, London, 2000); and Ouelette& Bzevanis, BIOINFORMATICS: A PRACTICAL GUIDE FOR ANALYSIS OF GENE ANDPROTEINS (Wiley & Sons, Inc., 2^(nd) ed., 2001); see also, U.S. Pat. No.6,420,108.

The present disclosure may also make use of various computer programproducts and software for a variety of purposes, such as probe design,management of data, analysis, and instrument operation. See U.S. Pat.Nos. 5,593,839; 5,795,716; 5,733,729; 5,974,164; 6,066,454; 6,090,555;6,185,561; 6,188,783; 6,223,127; 6,229,911 and 6,308,170. Additionally,the present disclosure may have embodiments that include methods forproviding genetic information over networks such as the Internet asshown in U.S. Ser. No. 10/197,621 (U.S. Pub. No. 20030097222); Ser. No.10/063,559 (U.S. Pub. No. 20020183936), Ser. No. 10/065,856 (U.S. Pub.No. 20030100995); Ser. No. 10/065,868 (U.S. Pub. No. 20030120432); Ser.No. 10/423,403 (U.S. Pub. No. 20040049354).

Techniques for analyzing such expression, activity, and/or sequence data(indeed any data obtained according to the disclosure) will often beimplemented using hardware, software or a combination thereof in one ormore computer systems or other processing systems capable ofeffectuating such analysis.

Thus one aspect of the present disclosure provides systems related tothe above methods of the disclosure. In one embodiment the disclosureprovides a system for determining gene expression in a tumor sample,comprising:

-   -   (1) a sample analyzer for determining the expression levels in a        sample of a panel of genes including at least 4 CCGs, wherein        the sample analyzer contains the sample, RNA from the sample and        expressed from the panel of genes, or DNA synthesized from said        RNA;    -   (2) a first computer program for        -   (a) receiving gene expression data on at least 4 test genes            selected from the panel of genes,        -   (b) weighting the determined expression of each of the test            genes with a predefined coefficient, and        -   (c) combining the weighted expression to provide a test            value, wherein the combined weight given to said at least 4            or 5 or 6 CCGs is at least 40% (or 50%, 60%, 70%, 80%, 90%,            95% or 100%) of the total weight given to the expression of            all of said plurality of test genes; and optionally    -   (3) a second computer program for comparing the test value to        one or more reference values each associated with a        predetermined degree of risk of cancer.        In some embodiments at least 20%, 50%, 75%, or 90% of said        plurality of test genes are CCGs. In some embodiments the sample        analyzer contains reagents for determining the expression levels        in the sample of said panel of genes including at least 4 CCGs.        In some embodiments the sample analyzer contains CCG-specific        reagents as described below.

In another embodiment the disclosure provides a system for determininggene expression in a tumor sample, comprising: (1) a sample analyzer fordetermining the expression levels of a panel of genes in a tumor sampleincluding at least 4 CCGs, wherein the sample analyzer contains thetumor sample which is from a patient identified as having prostatecancer, breast cancer, brain cancer, bladder cancer, or lung cancer, RNAfrom the sample and expressed from the panel of genes, or DNAsynthesized from said RNA; (2) a first computer program for (a)receiving gene expression data on at least 4 test genes selected fromthe panel of genes, (b) weighting the determined expression of each ofthe test genes with a predefined coefficient, and (c) combining theweighted expression to provide a test value, wherein the combined weightgiven to said at least 4 or 5 or 6 CCGs is at least 40% (or 50%, 60%,70%, 80%, 90%, 95% or 100%) of the total weight given to the expressionof all of said plurality of test genes; and optionally (3) a secondcomputer program for comparing the test value to one or more referencevalues each associated with a predetermined degree of risk of cancerrecurrence or progression of the prostate cancer, breast cancer, braincancer, bladder cancer, or lung cancer. In some embodiments at least20%, 50%, 75%, or 90% of said plurality of test genes are CCGs. In someembodiments the system comprises a computer program for determining thepatient's prognosis and/or determining (including quantifying) thepatient's degree of risk of cancer recurrence or progression based atleast in part on the comparison of the test value with said one or morereference values.

In some embodiments, the system further comprises a display moduledisplaying the comparison between the test value and the one or morereference values, or displaying a result of the comparing step, ordisplaying the patient's prognosis and/or degree of risk of cancerrecurrence or progression.

In a preferred embodiment, the amount of RNA transcribed from the panelof genes including test genes (and/or DNA reverse transcribed therefrom)is measured in the sample. In addition, the amount of RNA of one or morehousekeeping genes in the sample (and/or DNA reverse transcribedtherefrom) is also measured, and used to normalize or calibrate theexpression of the test genes, as described above.

In some embodiments, the plurality of test genes includes at least 2, 3or 4 CCGs, which constitute at least 50%, 75% or 80% of the plurality oftest genes, and preferably 100% of the plurality of test genes. In someembodiments, the plurality of test genes includes at least 5, 6 or 7, orat least 8 CCGs, which constitute at least 20%, 25%, 30%, 40%, 50%, 60%,70%, 75%, 80% or 90% of the plurality of test genes, and preferably 100%of the plurality of test genes. Thus in some embodiments the pluralityof test genes comprises at least some number of CCGs (e.g., at least 3,4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50 or more CCGs) andthis plurality of CCGs comprises the top 2, 3, 4, 5, 6, 7, 8, 9, 10, 11,12, 13, 14, 15, 20, 25, 30, 35, 40 or more CCGs listed in Tables 9-11, &13-14. In some embodiments the plurality of test genes comprises atleast some number of CCGs (e.g., at least 3, 4, 5, 6, 7, 8, 9, 10, 15,20, 25, 30, 35, 40, 45, 50 or more CCGs) and this plurality of CCGscomprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, or 20 of thefollowing genes: ASPM, BIRC5, BUB1B, CCNB2, CDC2, CDC20, CDCA8, CDKN3,CENPF, DLGAP5, FOXM1, KIAA0101, KIF11, KIF2C, KIF4A, MCM10, NUSAP1,PRC1, RACGAP1, and TPX2. In some embodiments the plurality of test genescomprises at least some number of CCGs (e.g., at least 3, 4, 5, 6, 7, 8,9, 10, 15, 20, 25, 30, 35, 40, 45, 50 or more CCGs) and this pluralityof CCGs comprises any one, two, three, four, five, six, seven, eight,nine, or ten or all of gene numbers 1 & 2, 1 to 3, 1 to 4, 1 to 5, 1 to6, 1 to 7, 1 to 8, 1 to 9, or 1 to 10 of any of Tables 9-11, & 13-14. Insome embodiments the plurality of test genes comprises at least somenumber of CCGs (e.g., at least 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30,35, 40, 45, 50 or more CCGs) and this plurality of CCGs comprises anyone, two, three, four, five, six, seven, eight, or nine or all of genenumbers 2 & 3, 2 to 4, 2 to 5, 2 to 6, 2 to 7, 2 to 8, 2 to 9, or 2 to10 of any of Tables 9-11, & 13-14. In some embodiments the plurality oftest genes comprises at least some number of CCGs (e.g., at least 3, 4,5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50 or more CCGs) and thisplurality of CCGs comprises any one, two, three, four, five, six, seven,or eight or all of gene numbers 3 & 4, 3 to 5, 3 to 6, 3 to 7, 3 to 8, 3to 9, or 3 to 10 of any of Tables 9-11, & 13-14. In some embodiments theplurality of test genes comprises at least some number of CCGs (e.g., atleast 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50 or moreCCGs) and this plurality of CCGs comprises any one, two, three, four,five, six, or seven or all of gene numbers 4 & 5, 4 to 6, 4 to 7, 4 to8, 4 to 9, or 4 to 10 of any of Tables 9-11, & 13-14. In someembodiments the plurality of test genes comprises at least some numberof CCGs (e.g., at least 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40,45, 50 or more CCGs) and this plurality of CCGs comprises any one, two,three, four, five, six, seven, eight, nine, 10, 11, 12, 13, 14, or 15 orall of gene numbers 1 & 2, 1 to 3, 1 to 4, 1 to 5, 1 to 6, 1 to 7, 1 to8, 1 to 9, 1 to 10, 1 to 11, 1 to 12, 1 to 13, 1 to 14, or 1 to 15 ofany of Tables 9-11, & 13-14.

In some other embodiments, the plurality of test genes includes at least8, 10, 12, 15, 20, 25 or 30 CCGs, which constitute at least 20%, 25%,30%, 40%, 50%, 60%, 70%, 75%, 80% or 90% of the plurality of test genes,and preferably 100% of the plurality of test genes.

The sample analyzer can be any instrument useful in determining geneexpression, including, e.g., a sequencing machine (e.g., IlluminaHiSeq™, Ion Torrent PGM, ABI SOLiD™ sequencer, PacBio RS, HelicosHeliscope™, etc.), a real-time PCR machine (e.g., ABI 7900, FluidigmBioMark™, etc.), a microarray instrument, etc.

In one aspect, the present disclosure provides methods of treating acancer patient comprising obtaining CCG status information (e.g., theCCGs in Table 1 or Panels A through G), and recommending, prescribing oradministering a treatment for the cancer patient based on the CCGstatus. In some embodiments, the method further includes obtainingclinical parameter information, and/or obtaining PTEN status informationfrom a sample from the patient and treating the patient with aparticular treatment based on the CCG status, clinical parameter and/orPTEN status information. For example, the disclosure provides a methodof treating a cancer patient comprising:

-   -   (1) determining the status of at least one CCG;    -   (2) determining the status of at least on clinical parameter;    -   (3) determining the status of PTEN in a sample obtained from the        patient; and    -   (4) recommending, prescribing or administering either        -   (a) an active (including aggressive) treatment if the            patient has at least one of increased expression of the CCG,            recurrence-associated clinical parameter, or low/negative            PTEN status, or        -   (b) a passive (or less aggressive) treatment if the patient            has none of increased expression of the CCG,            recurrence-associated clinical parameter, or low/negative            PTEN status.            In some embodiments, the determining steps comprise            receiving a report communicating the relevant status (e.g.,            CCG status). In some embodiments this report communicates            such status in a qualitative manner (e.g., “high” or            “increased” expression). In some embodiments this report            communicates such status indirectly by communicating a score            (e.g., prognosis score, recurrence score, combined score as            discussed above, etc.) that incorporates such status.

Whether a treatment is aggressive or not will generally depend on thecancer-type, the age of the patient, etc. For example, in breast canceradjuvant chemotherapy is a common aggressive treatment given tocomplement the less aggressive standards of surgery and hormonaltherapy. Those skilled in the art are familiar with various otheraggressive and less aggressive treatments for each type of cancer.“Active treatment” in prostate cancer is well-understood by thoseskilled in the art and, as used herein, has the conventional meaning inthe art. Generally speaking, active treatment in prostate cancer isanything other than “watchful waiting.” Active treatment currentlyapplied in the art of prostate cancer treatment includes, e.g.,prostatectomy, radiotherapy, hormonal therapy (e.g., GnRH antagonists,GnRH agonists, antiandrogens), chemotherapy, high intensity focusedultrasound (“HIFU”), etc. Each treatment option carries with it certainrisks as well as side-effects of varying severity, e.g., impotence,urinary incontinence, etc. Thus it is common for doctors, depending onthe age and general health of the man diagnosed with prostate cancer, torecommend a regime of “watchful-waiting.”

“Watchful-waiting,” also called “active surveillance,” also has itsconventional meaning in the art. This generally means observation andregular monitoring without invasive treatment. Watchful-waiting issometimes used, e.g., when an early stage, slow-growing prostate canceris found in an older man. Watchful-waiting may also be suggested whenthe risks of surgery, radiation therapy, or hormonal therapy outweighthe possible benefits. Other treatments can be started if symptomsdevelop, or if there are signs that the cancer growth is accelerating(e.g., rapidly rising PSA, increase in Gleason score on repeat biopsy,etc.).

Although men who choose watchful-waiting avoid the risks of surgery andradiation, watchful-waiting carries its own risks, e.g., increased riskof metastasis. For younger men, a trial of active surveillance may notmean avoiding treatment altogether, but may reasonably allow a delay ofa few years or more, during which time the quality of life impact ofactive treatment can be avoided. Published data to date suggest thatcarefully selected men will not miss a window for cure with thisapproach. Additional health problems that develop with advancing ageduring the observation period can also make it harder to undergo surgeryand radiation therapy. Thus it is clinically important to carefullydetermine which prostate cancer patients are good candidates forwatchful-waiting and which patients should receive active treatment.

Thus, the disclosure provides a method of treating a prostate cancerpatient or providing guidance to the treatment of a patient. In thismethod, the status of at least one CCG (e.g., those in Table 1 or PanelsA through G), at least one recurrence-associated clinical parameter,and/or the status of PTEN is determined, and (a) active treatment isrecommended, initiated or continued if a sample from the patient has anelevated status for at least one CCG, the patient has at least onerecurrence-associated clinical parameter, and/or low/negative PTENstatus, or (b) watchful-waiting is recommended/initiated/continued ifthe patient has neither an elevated status for at least one CCG, arecurrence-associated clinical parameter, nor low/negative PTEN status.In certain embodiments, CCG status, the clinical parameter(s) and PTENstatus may indicate not just that active treatment is recommended, butthat a particular active treatment is preferable for the patient(including relatively aggressive treatments such as, e.g., RP and/oradjuvant therapy).

In general, adjuvant therapy (e.g., chemotherapy, radiotherapy, HIFU,hormonal therapy, etc. after prostatectomy or radiotherapy) is not thestandard of care in prostate cancer. According to the presentdisclosure, however, physicians may be able to determine which prostatecancer patients have particularly aggressive disease and thus shouldreceive adjuvant therapy. Thus in one embodiment, the disclosureprovides a method of treating a patient (e.g., a prostate cancerpatient) comprising determining the status of at least one CCG (e.g.,those in Table 1 or Panels A through G), the status of at least onerecurrence-associated clinical parameter, and/or the status of PTEN andinitiating adjuvant therapy after prostatectomy or radiotherapy if asample from the patient has an elevated status for at least one CCG, thepatient has at least one recurrence-associated clinical parameter and/orthe patient has low/negative PTEN status.

In one aspect, the disclosure provides compositions for use in the abovemethods. Such compositions include, but are not limited to, nucleic acidprobes hybridizing to PTEN or a CCG (or to any nucleic acids encodedthereby or complementary thereto); nucleic acid primers and primer pairssuitable for amplifying all or a portion of PTEN or a CCG or any nucleicacids encoded thereby; antibodies binding immunologically to apolypeptide encoded by PTEN or a CCG; probe sets comprising a pluralityof said nucleic acid probes, nucleic acid primers, antibodies, and/orpolypeptides; microarrays comprising any of these; kits comprising anyof these; etc. In some aspects, the disclosure provides computermethods, systems, software and/or modules for use in the above methods.

In some embodiments the disclosure provides a probe comprising anisolated oligonucleotide capable of selectively hybridizing to PTEN orat least one of the genes in Table 1 or Panels A through G. The terms“probe” and “oligonucleotide” (also “oligo”), when used in the contextof nucleic acids, interchangeably refer to a relatively short nucleicacid fragment or sequence. The disclosure also provides primers usefulin the methods of the disclosure. “Primers” are probes capable, underthe right conditions and with the right companion reagents, ofselectively amplifying a target nucleic acid (e.g., a target gene). Inthe context of nucleic acids, “probe” is used herein to encompass“primer” since primers can generally also serve as probes.

The probe can generally be of any suitable size/length. In someembodiments the probe has a length from about 8 to 200, 15 to 150, 15 to100, 15 to 75, 15 to 60, or 20 to 55 bases in length. They can belabeled with detectable markers with any suitable detection markerincluding but not limited to, radioactive isotopes, fluorophores,biotin, enzymes (e.g., alkaline phosphatase), enzyme substrates, ligandsand antibodies, etc. See Jablonski et al., NUCLEIC ACIDS RES. (1986)14:6115-6128; Nguyen et al., BIOTECHNIQUES (1992) 13:116-123; Rigby etal., J. MOL. BIOL. (1977) 113:237-251. Indeed, probes may be modified inany conventional manner for various molecular biological applications.Techniques for producing and using such oligonucleotide probes areconventional in the art.

Probes according to the disclosure can be used in thehybridization/amplification/detection techniques discussed above. Thus,some embodiments of the disclosure comprise probe sets suitable for usein a microarray in detecting, amplifying and/or quantitating PTEN and/ora plurality of CCGs. In some embodiments the probe sets have a certainproportion of their probes directed to CCGs—e.g., a probe set consistingof 10%, 20%, 30%, 40%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%,96%, 97%, 98%, 99%, or 100% probes specific for CCGs. In someembodiments the probe set comprises probes directed to at least 1, 2, 3,4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 45, 50, 60, 70,80, 90, 100, 125, 150, 175, 200, 250, 300, 350, 400, 450, 500, 600, 700,or 800 or more, or all, of the genes in Table 1 or Panels A through G.Such probe sets can be incorporated into high-density arrays comprising5,000, 10,000, 20,000, 50,000, 100,000, 200,000, 300,000, 400,000,500,000, 600,000, 700,000, 800,000, 900,000, or 1,000,000 or moredifferent probes. In other embodiments the probe sets comprise primers(e.g., primer pairs) for amplifying nucleic acids comprising at least aportion of PTEN or of one or more of the CCGs in Table 1 or Panels Athrough G.

In another aspect of the present disclosure, a kit is provided forpracticing the prognosis of the present disclosure. The kit may includea carrier for the various components of the kit. The carrier can be acontainer or support, in the form of, e.g., bag, box, tube, rack, and isoptionally compartmentalized. The carrier may define an enclosedconfinement for safety purposes during shipment and storage. The kitincludes various components useful in determining the status of one ormore CCGs and one or more housekeeping gene markers, using theabove-discussed detection techniques. For example, the kit many includeoligonucleotides specifically hybridizing under high stringency to mRNAor cDNA of the genes in Table 1 or Panels A through G. Sucholigonucleotides can be used as PCR primers in RT-PCR reactions, orhybridization probes. In some embodiments the kit comprises reagents(e.g., probes, primers, and or antibodies) for determining theexpression level of a panel of genes, where said panel comprises atleast 25%, 30%, 40%, 50%, 60%, 75%, 80%, 90%, 95%, 99%, or 100% CCGs(e.g., CCGs in Table 1 or any of Panels A through G). In someembodiments the kit consists of reagents (e.g., probes, primers, and orantibodies) for determining the expression level of no more than 2500genes, wherein at least 5, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100,120, 150, 200, 250, or more of these genes are CCGs (e.g., CCGs in Table1 or any of Panels A through G).

The oligonucleotides in the detection kit can be labeled with anysuitable detection marker including but not limited to, radioactiveisotopes, fluorephores, biotin, enzymes (e.g., alkaline phosphatase),enzyme substrates, ligands and antibodies, etc. See Jablonski et al.,Nucleic Acids Res., 14:6115-6128 (1986); Nguyen et al., Biotechniques,13:116-123 (1992); Rigby et al., J. Mol. Biol., 113:237-251 (1977).Alternatively, the oligonucleotides included in the kit are not labeled,and instead, one or more markers are provided in the kit so that usersmay label the oligonucleotides at the time of use.

In another embodiment of the disclosure, the detection kit contains oneor more antibodies selectively immunoreactive with one or more proteinsencoded by PTEN or one or more CCGs or optionally any additionalmarkers. Examples include antibodies that bind immunologically to PTENor a protein encoded by a gene in Table 1 or Panels A through G. Methodsfor producing and using such antibodies have been described above indetail.

Various other components useful in the detection techniques may also beincluded in the detection kit of this disclosure. Examples of suchcomponents include, but are not limited to, Taq polymerase,deoxyribonucleotides, dideoxyribonucleotides, other primers suitable forthe amplification of a target DNA sequence, RNase A, and the like. Inaddition, the detection kit preferably includes instructions on usingthe kit for practice the prognosis method of the present disclosureusing human samples.

Specific Embodiments

Two specific embodiments of the disclosure for use in biopsy andprostatectomy samples are show below. Those skilled in the art willunderstand that each element of these processes may be altered whileretaining the essential features and accomplishing the same goals.

Biopsy

Indications and Use

Formalin-fixed paraffin-embedded (FFPE) tissue from blocks or slides ofprostatic adenocarcinoma biopsies may be used. Blocks may include atleast 2 mm of tumor on diagnostic H&E slides for sample processing andRNA extraction. In cases where blocks are not available, one 3-5 μm H&Eslide followed by ten consecutive 10 μm unstained slides and a final H&Eslide may be acceptable. Sample barcodes, which are scanned and tracked,may be applied to each block (or slide). The H&E slides from each casemay be evaluated, e.g., by a pathologist, to determine the location andamount of tumor per slide. Using the H&E stained slides as a guide,tumor tissue may be removed from ten unstained slides and total RNA maybe extracted from the tissue. The expression of the genes in any ofPanels A-F, normalized to that of housekeeping genes, may then bemeasured in triplicate to generate a test value (e.g., CCP score).

As an optional quality control measure, a no-RNA control and a normalhuman RNA control with a previously determined CCP score may be analyzedwithin each sample run. Controls may be analyzed to verify expectedresults.

Performance Characteristics/Limitations

The CCP score may be used alone or in combination with clinicalinformation to arrive at a clinical prognosis. The CCP score may becombined with the patient's CAPRA nomogram score (see Cooperberg et al.,J. Natl. Cancer Inst. (2009) 101(12):878-887 for details on the CAPRAnomogram) according to the following equation: Combinedscore=(0.58*CCP+0.41*CAPRA).

Clinically Reportable Range

A clinically reportable CCP score range of −1.3 to 4.7 may be applied. Ascale of CCP scores may be reported for the American UrologicalAssociation (AUA) risk category of the individual patient. The scale mayconsist of five 1-unit intervals, with the middle interval beingcentered at the median CCP score for that specific AUA risk category inthe U.S. population. There may be approximately a 2-fold change in riskof prostate cancer mortality between intervals, which would be thehazard ratio corresponding to a 1-unit change in the CCP score.

Detection Limit/Linearity

CCP scores between −3.0 and +7.0 may represent the range of scoresdetectable by the assay. Linearity may be established within in thisrange as follows: The relevant genes may be pre-amplified, diluted to 7different concentrations and spiked into a cDNA sample of knownconcentration. Each spiked sample may then be assayed in triplicate, andthe resulting 3 data points may be averaged for each concentration togenerate a CCP score.

Interference

In some cases adjuvant hormonal therapy and radiation treatment mayaffect CCP scores. Thus, in some embodiments the method is applied onlyto patients who have not received these treatments prior to biopsy.

Limitations

In some embodiments only human FFPE prostate tumor specimens areanalyzed.

Interpretive Criteria

CCP Scores within the Technical Range of the Assay and within the Rangeof Scores for which Clinical Prediction is Validated (e.g., Between −1.3and 4.7)

The estimated prostate cancer-specific mortality risk may be providedfor each CCP score within this range, and in some cases may show how theCCP score differentiates between patients with the same CAPRA score. Inaddition, the U.S Distribution Percentile for CCP scores may beprovided, e.g., for patients in the same CAPRA risk category (low,intermediate, or high). Although the risk percentage may be given acrossthe full range, example risk scores are given below:

CCP Likelihood of Cancer- Score Specific Death −1  5.9% 0 11.6% 1   22%2 39.5% 3 63.8% 4 87.2%CCP Scores within the Technical Range of the Assay but Outside the Rangeof Scores for which Clinical Prediction is Validated (e.g., −1.3 butGreater than −3.0)

If linearity of CCP scores within such a range have been established,then the calculated CCP score may be reported but in some cases theestimated prostate cancer-specific relative mortality risk may not beprovided (in some cases the U.S Distribution Percentile for CCP scores,e.g., for patients in the same CAPRA risk category (low, intermediate,or high), may be reported).

CCP Scores Outside the Technical Range of the Assay (e.g., Greater than4.7 or Less than 7.0)

These scores may lie outside of the verified detection limits of thisassay and may represent an artifact or technical error. Thus, in somecases these scores may not be reportable.

Post-Prostatectomy

Indications and Use

Formalin-fixed paraffin-embedded (FFPE) tissue from prostatectomy blocksof prostatic adenocarcinoma may be used. Blocks may include at least 5mm of tumor on diagnostic H&E slides for sample processing and RNAextraction. In cases where blocks are not available, one 3-5 μm H&Eslide followed by five consecutive 10 μm unstained slides and a finalH&E slide may be acceptable. Sample barcodes, which are scanned andtracked, may be applied to each block (or slide). The H&E slides fromeach case may be evaluated, e.g., by a pathologist, to determine thelocation and amount of tumor per slide. Using the H&E stained slides asa guide, tumor tissue may be removed from five unstained slides andtotal RNA may be extracted from the tissue.

The expression of the genes in any of Panels A-F, normalized to that ofhousekeeping genes, may then be measured in triplicate to generate atest value (e.g., CCP score). This CCP score can be used to estimateprobability of recurrence (e.g., biochemical recurrence) within a giventime period (e.g., within 10 years after surgery). A patient's CCP scorecan also be compared with the CCP scores of other patients within a U.S.distribution of scores previously observed. For a more accurateestimation of 10-year biochemical recurrence risk, clinical informationprovided by the healthcare provider may be used to calculate a nomogramscore. The CCP score may then be combined with the nomogram score togenerate a combined score. This combined score may be used to estimatethe 10-year risk of biochemical recurrence, and it can be compared withthe combined scores of other patients within a U.S. distribution ofscores. In some embodiments, the combined score is only communicated tothe healthcare provider if all required clinical information has beenprovided and, if all required clinical parameters are not provided onthe test request form, only the Prolaris Score is reported. In some suchembodiments, the combined score may be obtained by inputting therequired clinical information subsequent to the reporting of the CCPscore by entering clinical parameters required for the nomogram alongwith the patient's CCP score.

As an optional quality control measure, a no-RNA control and a normalhuman RNA control with a previously determined CCP score may be analyzedwithin each sample run. Controls may be analyzed to verify expectedresults.

Performance Characteristics/Limitations

Clinically Reportable Ranges

A clinically reportable CCP score range of −1.6 to 3.7 may be applied.Individuals with a CCP score of 1.2 or higher may be deemed to have apredicted probability of biochemical recurrence by 10 years of greaterthan 50%. CCP scores outside the range of −1.6 to 3.7 may be reportedbut may be qualified with the information that they lie outside therange of the prediction model.

Similarly, a clinically reportable combined score range of −0.9 to 4.5may be applied for combined scores. Individuals with a combined score of2.0 or higher may be deemed to have a predicted probability ofbiochemical recurrence by 10 years of greater than 50%. Combined scoresoutside of this range may be reported but may be qualified with theinformation that they lie outside the range of the prediction model.

Detection Limit/Linearity

CCP scores between −8 and 8 are technically detectable by the assay.Linearity may be established within this range as follows: The relevantgenes may be pre-amplified, diluted to different concentrations andspiked into a cDNA sample of known concentration. Each spiked sample maybe assayed in triplicate, and the resulting 3 data points maybe averagedfor each concentration to generate a Recurrence score. Linearity may beestablished for CCP scores ranging from 0 to 8 using this method.Linearity for CCP scores ranging from −8 to 0 may be similarlyestablished.

Interference

In some cases neoadjuvant hormonal therapy and radiation treatment mayaffect CCP scores. Thus, in some embodiments the method is applied onlyto patients who have not received these treatments prior to surgery.

Limitations

In some embodiments only human FFPE prostate tumor specimens areanalyzed. In some embodiments only samples from patients with PSA levels≤100 ng/ml are analyzed. In some embodiments only samples yielding atleast 125 ng of RNA are analyzed.

Interpretive Criteria

Scores within the Technical Range of the Assay and within the Range ofScores for which Clinical Prediction is Validated (e.g., 1.6 to 3.7 forCCP Scores; −0.9 to 4.5 for Combined Scores)

Both CCP scores and combined scores within this range may be reportedtogether with predicted probability of recurrence. Although the riskpercentage may be given continuously across the full range, example riskscores are given below:

CCP Likelihood of Score Recurrence −1 12.6% 0 24.9% 1 45.5% 2 72.5% 393.6%

Combined Likelihood of Score Recurrence 0 11.5% 1  25% 2 49.3% 3 79.8% 497.7%Scores within the Technical Range of the Assay but Outside the Range ofScores for which Clinical Prediction is Validated (e.g., −8 to 1.7 and3.8 to 8 for CCP; −8 to −1.0 and 4.6 to 8 for Combined Scores)

If linearity of CCP scores and combined scores within such a range hasbeen established, then the calculated CCP score or combined score may bereported but in some cases the estimated recurrence risk may not beprovided.

Scores Outside the Technical Range of the Assay (e.g., Less than −8 orGreater than 8 for CCP or Combined Scores)

These scores may lie outside of the verified detection limits of thisassay and may represent an artifact or technical error. Thus, in somecases these scores may not be reportable.

Additional Specific Embodiments

The following paragraphs describe numerous additional specificembodiments of the present disclosure.

Embodiment 1

A method for determining a test patient's likelihood of cancerrecurrence or cancer-specific death, comprising:

-   -   (1) measuring, in a sample obtained from said test patient, the        expression levels of a panel of genes comprising at least 3 test        genes selected from Panel F;    -   (2) providing a test expression score by (a) weighting the        determined expression of each gene in said panel of genes with a        predefined coefficient (which may be 0), and (b) combining the        weighted expression of each gene in said panel of genes to        provide said test expression score, wherein said test genes are        weighted to contribute at least 25% to said test expression        score; and    -   (3) diagnosing said test patient as having either (a) an        increased likelihood of cancer recurrence or cancer-specific        death based at least in part on said test expression score        exceeding a first reference expression score or (b) no increased        likelihood of cancer recurrence or cancer-specific death based        at least in part on said test expression score not exceeding a        second reference expression score.

Embodiment 2

The method of Embodiment 1, wherein said test genes are weighted tocontribute at least 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 96%, 97%,98%, 99%, or 100% of the total weight given to the expression of all ofsaid panel of genes in said test expression score.

Embodiment 3

The method of either Embodiment 1 or Embodiment 2, wherein said panel ofgenes comprises at least 4, 5, 6, 7, 8, 9, 10, 12, 14, 16, 18, 20, 22,24, 26, 28, 30 or 31 test genes selected from Panel F.

Embodiment 4

The method of any one of Embodiments 1 to 3, wherein said test genescomprise at least the top 3, 4, 5, 6, 7, 8, 9, 10, 12, 14, 16, 18, 20,22, 24, 26, 28, 30 genes in Panel F.

Embodiment 5

The method of any one of Embodiments 1 to 4, wherein said test genesfurther comprise KLK3 and KLK3 expression is incorporated into said testexpression score such that decreased KLK3 expression increases saidscore.

Embodiment 6

The method of any one of Embodiments 1 to 5, wherein said test genesfurther comprise PTEN.

Embodiment 7

The method of any one of Embodiments 1 to 6, wherein said measuring stepcomprises:

-   -   measuring the amount of panel mRNA in said sample transcribed        from each of between 3 and 500 panel genes, or measuring the        amount of cDNA reverse transcribed from said panel mRNA; and    -   measuring the amount of housekeeping mRNA in said sample        transcribed from one or more housekeeping genes, or measuring        the amount of cDNA reverse transcribed from said housekeeping        mRNA.

Embodiment 8

The method of any one of Embodiments 1 to 7, wherein said first andsecond reference expression scores are the same.

Embodiment 9

The method of any one of Embodiments 1 to 8, wherein half of cancerpatients in a reference population have an expression score exceedingsaid first reference expression score and half of cancer patients insaid reference population have an expression score not exceeding saidfirst reference expression score.

Embodiment 10

The method of any one of Embodiments 1 to 7, wherein one third of cancerpatients in a reference population have an expression score exceedingsaid first reference expression score and one third of cancer patientsin said reference population have an expression score not exceeding saidsecond reference expression score.

Embodiment 11

The method of Embodiment 10, comprising diagnosing said test patient ashaving (a) an increased likelihood of cancer recurrence orcancer-specific death if said test expression score exceeds said firstreference expression score; (b) a decreased likelihood of cancerrecurrence or cancer-specific death if said test expression score doesnot exceed said second reference expression score; or (c) neitherincreased nor decreased (i.e., consistent) likelihood of cancerrecurrence or cancer-specific death if said test expression scoreexceeds said second reference expression score but does not exceed saidfirst reference expression score.

Embodiment 12

The method of any one of Embodiments 1 to 11, wherein cancer recurrenceis chosen from the group consisting of distant metastasis of the primarycancer; local metastasis of the primary cancer; recurrence of theprimary cancer; progression of the primary cancer; and development oflocally advanced, metastatic disease.

Embodiment 13

A method for determining a cancer patient's likelihood of cancerrecurrence or cancer-specific death, comprising:

-   -   (1) measuring, in a sample obtained from said patient, the        expression levels of a panel of genes comprising at least 3 test        genes selected from Panel F;    -   (2) providing a test expression score by (1) weighting the        determined expression of each gene in said panel of genes with a        predefined coefficient (which may be 0), and (2) combining the        weighted expression to provide said test expression score,        wherein said test genes are weighted to contribute at least 25%        to said test expression score;    -   (3) providing a test prognostic score combining said test        expression score with at least one test clinical score        representing at least one clinical variable; and    -   (4) diagnosing said patient as having either (a) an increased        likelihood of cancer recurrence or cancer-specific death based        at least in part on said test prognostic score exceeding a first        reference prognostic score or (b) no increased likelihood of        cancer recurrence or cancer-specific death based at least in        part on said test prognostic score not exceeding a second        reference prognostic.

Embodiment 14

The method of Embodiment 13, wherein said at least one clinical scoreincorporates at least one clinical variable chosen from the groupconsisting of year of RP, surgical margins, extracapsular extension,seminal vesicle invasion, lymph node involvement, primary Gleason score,secondary Gleason score, or preoperative PSA.

Embodiment 15

The method of either Embodiment 13 or Embodiment 14, wherein saidprognostic scores incorporate (a) a first clinical score representingpreoperative PSA concentration, optionally incorporated as a numericalconcentration of ng/dL transformed by the natural logarithm, adding 1 toavoid zero values; and (b) a second clinical score representing Gleasonscore, optionally incorporated as a continuous numeric variable orcategorized as <7 (reference level), 7, or >7.

Embodiment 16

The method of any one of Embodiments 13 to 15, wherein said prognosticscores are calculated according to a formula comprising the followingterms: (A×expression score)+(B×clinical score).

Embodiment 17

The method of Embodiment 16, wherein A=0.58, said clinical score isCAPRA score, and B=0.41.

Embodiment 18

An in vitro method of classifying cancer comprising:

-   -   (1) determining the expression of a panel of genes comprising at        least 4 CCGs from Table 2 in a sample;    -   (2) providing a test value by        -   (a) weighting the determined expression of each of a            plurality of test genes selected from the panel of            biomarkers with a predefined coefficient, wherein said            plurality of test genes comprises said CCGs; and        -   (b) combining the weighted expression to provide the test            value, wherein the combined weight given to said CCGs is at            least 40% of the total weight given to the expression of            said plurality of test genes; and    -   (3) correlating said test value to        -   (a) an unfavorable cancer classification if said test value            is representative of high expression of the plurality of            test genes; or        -   (b) a favorable cancer classification if said test value is            representative of low or normal expression of the plurality            of test genes.

Embodiment 19

The method of Embodiment 18, wherein at least 75% of said plurality oftest genes are CCGs.

Embodiment 20

The method of Embodiment 19, wherein said panel of genes and saidplurality of test genes comprise the top 5 genes in any one of Tables9-11, & 13-14.

Embodiment 21

The method of Embodiment 20, wherein said panel of genes and saidplurality of test genes comprise the genes in any one of Tables 1, 2,7-11, 13-14 and/or Y or Panels A through I.

Embodiment 22

The method of Embodiment 21, wherein said unfavorable cancerclassification is chosen from the group consisting of (a) a poorprognosis, (b) an increased likelihood of cancer progression, (c) anincreased likelihood of cancer recurrence (e.g., biochemicalrecurrence), (d) an increased likelihood of cancer-specific death, or(e) a decreased likelihood of response to treatment with a particularregimen.

Embodiment 23

The method of Embodiment 22, wherein said unfavorable cancerclassification is an increased likelihood of cancer recurrence.

Embodiment 24

The method of Embodiment 22, wherein said unfavorable cancerclassification is an increased likelihood of cancer-specific death.

Embodiment 25

The method of Embodiment 18, wherein said favorable cancerclassification is chosen from the group consisting of (a) a goodprognosis, (b) no increased likelihood of cancer progression, (c) noincreased likelihood of cancer recurrence, (d) no increased likelihoodof cancer-specific death, or (e) an increased likelihood of response totreatment with a particular regimen.

Embodiment 26

The method of Embodiment 25, wherein said favorable cancerclassification is no increased likelihood of cancer recurrence.

Embodiment 27

The method of Embodiment 25, wherein said favorable cancerclassification is no increased likelihood of cancer-specific death.

Embodiment 28

A method of determining gene expression in a tumor sample, comprising:

-   -   (1) obtaining a tumor sample from a patient identified as having        prostate cancer, lung cancer, bladder cancer or brain cancer;    -   (2) determining the expression levels of a panel of genes in        said tumor sample including at least 4 cell-cycle genes; and    -   (3) providing a test value by (a) weighting the determined        expression of each of a plurality of test genes selected from        said panel of genes with a predefined coefficient, and (b)        combining the weighted expression to provide said test value,        wherein at least 75%, at least 85% or at least 95% of said        plurality of test genes are cell-cycle genes.

Embodiment 29

The method of Embodiment 28, wherein at least 90% of said plurality oftest genes are cell-cycle genes.

Embodiment 30

The method of Embodiment 28 or 29, wherein said determining stepcomprises:

-   -   measuring the amount of mRNA in said tumor sample transcribed        from each of between 6 and 200 cell-cycle genes; and    -   measuring the amount of mRNA of one or more housekeeping genes        in said tumor sample.

Embodiment 31

The method of Embodiment 28 or 29 or 30, wherein the expression of atleast 8 cell-cycle genes are determined and weighted.

Embodiment 32

A method of prognosing prostate cancer, lung cancer, bladder cancer orbrain cancer, comprising:

-   -   (1) determining in a tumor sample from a patient diagnosed of        prostate cancer, lung cancer, bladder cancer or brain cancer,        the expression of a panel of genes in said tumor sample        including at least 4 cell-cycle genes;    -   (2) providing a test value by (1) weighting the determined        expression of each of a plurality of test genes selected from        said panel of genes with a predefined coefficient, and (2)        combining the weighted expression to provide said test value,        wherein at least 75%, at least 85% or at least 95% of said        plurality of test genes are cell-cycle genes; and    -   (3) correlating an increased level of expression of said        plurality of test genes to a poor prognosis.

Embodiment 33

The prognosis method of Embodiment 32, further comprising comparing saidtest value to a reference value, and correlating to an increasedlikelihood of poor prognosis if said test value is greater than saidreference value.

Embodiment 34

The prognosis method of Embodiment 32, wherein the expression levels offrom 6 to about 200 cell-cycle genes are measured.

Embodiment 35

The method of any one of Embodiment 32 to 34, wherein said determiningstep comprises:

-   -   measuring the amount of mRNA of from 6 to about 200 cell-cycle        genes in said tumor sample; and    -   measuring the amount of mRNA of one or more housekeeping genes        in said tumor sample.

Embodiment 36

A method of treating cancer in a patient identified as having prostatecancer, lung cancer, bladder cancer or brain cancer, comprising:

-   -   (1) determining in a tumor sample from a patient diagnosed of        prostate cancer, lung cancer, bladder cancer or brain cancer,        the expression of a panel of genes in said tumor sample        including at least 4 cell-cycle genes;    -   (2) providing a test value by (1) weighting the determined        expression of each of a plurality of test genes selected from        said panel of genes with a predefined coefficient, and (2)        combining the weighted expression to provide said test value,        wherein at least 60% or 75% of said plurality of test genes are        cell-cycle genes, wherein an increased level of expression of        said plurality of test genes indicates a poor prognosis; and    -   (3) administering to said patient an anti-cancer drug, or        recommending or prescribing or initiating active treatment if a        poor prognosis is determined.

Embodiment 37

A diagnostic kit for prognosing cancer in a patient diagnosed ofprostate cancer, lung cancer, bladder cancer or brain cancer,comprising, in a compartmentalized container:

-   -   (1) a plurality of PCR primer pairs for PCR amplification of at        least 5 test genes, wherein less than 10%, 30% or less than 40%        of all of said at least 8 test genes are non-cell-cycle genes;        and    -   (2) one or more PCR primer pairs for PCR amplification of at        least one housekeeping gene.

Embodiment 38

A diagnostic kit for prognosing cancer in a patient diagnosed ofprostate cancer, lung cancer, bladder cancer or brain cancer,comprising, in a compartmentalized container:

-   -   (1) a plurality of probes for hybridizing to at least 5 test        genes under stringent hybridization conditions, wherein less        than 10%, 30% or less than 40% of all of said at least 8 test        genes are non-cell-cycle genes; and    -   (2) one or more probes for hybridizing to at least one        housekeeping gene.

Embodiment 39

A kit consisting essentially of, in a compartmentalized container:

-   -   (1) a first plurality of PCR reaction mixtures for PCR        amplification of between 5 or 10 and 300 test genes, wherein at        least 50%, at least 60% or at least 80% of said 5 or 10 to 300        test genes are cell-cycle genes, and wherein each reaction        mixture comprises a PCR primer pair for PCR amplifying one of        said test genes; and    -   (2) a second plurality of PCR reaction mixtures for PCR        amplification of at least one housekeeping gene.

Embodiment 40

The kit of any one of Embodiments 37 to 39, wherein cell-cycle genesconstitute no less than 10% of the total number of said test genes.

Embodiment 41

The kit of any one of Embodiments 37 to 39, wherein cell-cycle genesconstitute no less than 20% of the total number of said test genes.

Embodiment 42

Use of

-   -   (1) a plurality of PCR primer pairs suitable for PCR        amplification of at least 4 cell-cycle genes; and    -   (2) one or more PCR primer pairs suitable for PCR amplification        of at least one housekeeping gene,    -   for the manufacture of a diagnostic product for determining the        expression of said test genes in a tumor sample from a patient        diagnosed of prostate cancer, lung cancer, bladder cancer or        brain cancer, to predict the prognosis of cancer, wherein an        increased level of said expression indicates a poor prognosis or        an increased likelihood of recurrence of cancer in the patient.

Embodiment 43

The use of Embodiment 42, wherein said plurality of PCR primer pairs aresuitable for PCR amplification of at least 8 cell-cycle genes.

Embodiment 44

The use of Embodiment 42 or 43, wherein said plurality of PCR primerpairs are suitable for PCR amplification of from 4 to about 300 testgenes, no greater than 10%, 30% or less than 50% of which beingnon-cell-cycle genes.

Embodiment 45

The use of Embodiment 42 or 43, wherein said plurality of PCR primerpairs are suitable for PCR amplification of from 20 to about 300 testgenes, at least 25% of which being cell-cycle genes.

Embodiment 46

Use of

-   -   (1) a plurality of probes for hybridizing to at least 4        cell-cycle genes under stringent hybridization conditions; and    -   (2) one or more probes for hybridizing to at least one        housekeeping gene under stringent hybridization conditions,    -   for the manufacture of a diagnostic product for determining the        expression of said test genes in a tumor sample from a patient        diagnosed of prostate cancer, lung cancer, bladder cancer or        brain cancer, to predict the prognosis of cancer, wherein an        increased level of said expression indicates a poor prognosis or        an increased likelihood of recurrence of cancer in the patient.

Embodiment 47

The use of Embodiment 46, wherein said plurality of probes are suitablefor hybridization to at least 8 different cell-cycle genes.

Embodiment 48

The use of Embodiment 46 or 47, wherein said plurality of probes aresuitable for hybridization to from 4 to about 300 test genes, no greaterthan 10%, 30% or less than 50% of which being non-cell-cycle genes.

Embodiment 49

The use of Embodiment 46 or 47, wherein said plurality of probes aresuitable for hybridization to from 20 to about 300 test genes, at least25% of which being cell-cycle genes.

Embodiment 50

A system for prognosing cancer selected from prostate cancer, lungcancer, bladder cancer or brain cancer, comprising:

-   -   (1) a sample analyzer for determining the expression levels of a        panel of genes in said tumor sample including at least 4        cell-cycle genes, wherein the sample analyzer contains the tumor        sample which is from a patient identified as having prostate        cancer, lung cancer, bladder cancer or brain cancer, or cDNA        molecules from mRNA expressed from the panel of genes; and    -   (2) a first computer program for (a) receiving gene expression        data on at least 4 test genes selected from the panel of        genes, (b) weighting the determined expression of each of the        test genes, and (c) combining the weighted expression to provide        a test value, wherein at least 50%, at least at least 75% of at        least 4 test genes are cell-cycle genes; and    -   (3) a second computer program for comparing the test value to        one or more reference values each associated with a        predetermined degree of risk of cancer recurrence or progression        of the prostate cancer, lung cancer, bladder cancer or brain        cancer.

Embodiment 51

The system of Embodiment 50, further comprising a display moduledisplaying the comparison between the test value to the one or morereference values, or displaying a result of the comparing step.

Embodiment 52

The method of any one of Embodiments 1 to 36, wherein said cancer isprostate cancer, wherein said panel of genes or panel of test genesfurther comprises KLK3.

Embodiment 53

The method of Embodiment 52, wherein KLK3 expression is incorporatedinto said test expression score such that decreased KLK3 expressionincreases said test expression score.

Embodiment 54

The method of Embodiment 52, wherein KLK3 expression is incorporatedinto said test expression score such that decreased KLK3 expressioncorrelates to a test expression score that yields a diagnosis ofincreased likelihood of cancer recurrence or cancer-specific death.

Embodiment 55

The method of Embodiment 53, wherein said test expression scoreincorporates the negative of the numerical value of KLK3 expression suchthat a higher test expression score yields a diagnosis of increasedlikelihood of cancer recurrence or cancer-specific death.

Embodiment 56

A method of evaluating a patient's AUA prostate cancer riskclassification comprising:

-   -   (1) obtaining said patient's AUA prostate cancer risk        classification (as described in Example 8);    -   (2) providing a test value by        -   (a) weighting the determined expression of each of a            plurality of test genes selected from the panel of            biomarkers with a predefined coefficient, wherein said            plurality of test genes comprises said CCGs; and        -   (b) combining the weighted expression to provide the test            value, wherein the combined weight given to said CCGs is at            least 40% of the total weight given to the expression of            said plurality of test genes; and    -   (3)(a) reclassifying said patient as having a risk higher than        that indicated by the AUA classification if said test value is        greater than the median test value (e.g., at least 1%, 2%, 3%,        4%, 5%, 6%, 7%, 8%, 9%, 10% 15% 20% or 25% greater than the        median test value) for all patients in a reference population        having the same AUA classification; or    -   (3)(b) reclassifying said patient as having a risk lower than        that indicated by the AUA classification if said test value is        less than the median test value (e.g., at least 1%, 2%, 3%, 4%,        5%, 6%, 7%, 8%, 9%, 10% 15% 20% or 25% less than the median test        value) for all patients in a reference population having the        same AUA classification; or    -   (3)(c) confirming said patient's AUA classification if said test        value is substantially the same as the median test value (e.g.,        within 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10% 15% 20% or 25% of        the median test value) for all patients in a reference        population having the same AUA classification.

Embodiment 57

The method of embodiment 1, wherein said test genes further comprisePCA3 and PCA3 expression is incorporated into said test expression scoresuch that abnormal PCA3 expression increases said score.

Embodiment 58

The method of Embodiment 1, wherein said cancer is prostate cancer,wherein said panel of genes or panel of test genes further comprisesPCA3.

Embodiment 59

The method of Embodiment 58, wherein PCA3 expression is incorporatedinto said test expression score such that abnormal PCA3 expressionincreases said test expression score.

Embodiment 60

The method of Embodiment 58, wherein PCA3 expression is incorporatedinto said test expression score such that abnormal PCA3 expressioncorrelates to a test expression score that yields a diagnosis ofincreased likelihood of cancer recurrence or cancer-specific death.

Embodiment 61

The method Embodiment 1, wherein said test genes further comprise one ormore AR signaling genes.

Embodiment 62

The method of Embodiment 1, wherein said test genes further comprise oneor more AR sensitive genes.

Example 1

The following cell cycle gene (CCG) signature was tested for predictingtime to chemical recurrence after radical prostatectomy.

TABLE A 31-CCG Prostate Recurrence Signature AURKA BUB1 CCNB1 CCNB2 CDC2CDC20 CDC45L CDCA8 CENPA CKS2 DLG7 DTL FOXM1 HMMR KIF23 KPNA2 MAD2L1MELK MYBL2 NUSAP1 PBK PRC1 PTTG1 RRM2 TIMELESS TPX2 TRIP13 TTK UBE2CUBE2S ZWINT

Mean mRNA expression for the above 31 CCGs was tested on 440 prostatetumor FFPE samples using a Cox Proportional Hazard model in Splus 7.1(Insightful, Inc., Seattle Wash.). The p-value for the likelihood ratiotest was 3.98×10⁻⁵.

The mean of CCG expression is robust to measurement error and individualvariation between genes. In order to determine the optimal number ofcell cycle genes for the signature, the predictive power of the mean wastested for randomly selected sets of from 1 to 30 of the CCGs listedabove. This simulation showed that there is a threshold number of CCGsin a panel that provides significantly improved predictive power.

Example 2

In a univariate analysis a set of 31 CCGs (Table 7) was found to be asignificant predictor of biochemical recurrence (p-value=1.8×10⁻⁹) afterRP in prostate cancer patients. This signature was further evaluated todetermine whether it added to an established clinical nomogram forprostate cancer recurrence (the Kattan-Stephenson nomogram). In summary,the nomogram was a highly significant predictor of recurrence (p-value1.6×10⁻¹⁰) and, after adjusting for the nomogram, the CCG signature wasa significant predictor of biochemical recurrence (p-value 4.8×10⁻⁵,Table C).

Patients and Methods

Eight hundred four consecutive RP patients were followed for a median of9.5 years. The patient characteristics and the treatment outcomes of theentire cohort have been previously reported (Swanson et al., UROL ONCOL.(2007) 25:110-114). Tissue blocks and/or slides from the finalpathological evaluation with enough tissue for analysis were availablefor 430 patients. The cohort was divided randomly into 212 patientsutilized for a training and 199 patient samples as a validation set.

Gene Expression (Statistical Methods):

Association between biochemical recurrence and CCG expression wasevaluated using Cox PH models for time to recurrence. All of thep-values reported in this study were derived from a likelihood ratiotest comparing the null model to the model containing the test variable.A set of 31 CCGs (Table 7, supra) was randomly selected. The assays wereused to generate expression data from 212 patients in the training set.All of the expression data were generated in triplicate. The expressiondata were combined into a signature by calculating the mean expressionlevel for 26 CCGs. Association between biochemical recurrence and CCGexpression was evaluated using Cox PH models for time to recurrence.

Sample Preparation and Study Design:

RNA was isolated from FFPE tumor sections derived from 411 prostatecancer patients treated with RP. Representative 10 μm thick tumorsections were used to isolate RNA. When necessary, a pathologist guidedmacro- or micro-dissection of the sample was used to enrich for tumortissue before RNA isolation. None of the samples in the validationcohort were micro-dissected. Prior to any analysis, the cohort was splitinto 212 patients for initial characterization of the signature(“training set”) and 199 patients for validation. The clinicalcharacteristics of the training and validation cohort are listed onTable B.

TABLE B Training Validation p-value Statistic Age in years at RP, mean(sd) 67.3 (5.9)  66.8 (5.8)  0.355 t-test Ethnicity (% non-white) 2.80%7.60% 0.042 Fisher's exact Dissection method (% lcm)   24%   0% NA NARecurrence (%) 71/212 (33.5%) 72/199 (36.2%) 0.605 Fisher's exact Daysto recurrence, median 910 822 0.463 t-test Days to follow-up, median3373 3387 0.173 t-test Pre-surgery PSA (median) 7.3 6.8 0.163 t-test oflog Seminal vesicle 23/212 (10.8%) 28/199 (14.1%) 0.37 Fisher's exactBladder 12/212 (5.7%)  17/199 (8.5%)  0.335 Fisher's exact Lymph node8/212 (3.8%) 10/199 (5.0%)  0.632 Fisher's exact Capsular 100/212(47.2%)  101/199 (50.8%)  0.49 Fisher's exact Through capsule 59/212(27.8%) 66/199 (33.2%) 0.283 Fisher's exact Positive margins 43/212(20.3%) 57/199 (28.6%) 0.051 Fisher's exact Post-RP Gleason score >680/212 (37.7%) 66/199 (33.2%) 0.354 Fisher's exact Post-RP nomogram,mean (sd)  137 (19.5)  138 (23.0) 0.424 t-testResults

The CCG expression signature (Table 7, supra) was predictive of diseaserecurrence in a univariate analysis (p-value=1.8×10⁻⁹, Table C). Thedistribution of the signature score was skewed toward higher values(lower expression). The median value of signature score was used todivide the training cohort into two groups containing samples witheither high or low CCG expression. The survival versus time for bothgroups is shown in FIG. 2.

Predictive power of the CCG signature after accounting for clinicalvariables typically included in a post-surgical nomogram (theKattan-Stephenson nomogram) was also evaluated. The nomogram was ahighly significant predictor of recurrence (p-value)1.6×10¹⁰. Afteradjusting for the nomogram, the CCG signature was a significantpredictor of biochemical recurrence (FIG. 3) in the discovery cohort(p-value 0.03) and in the clinical validation cohort (p-value 4.8×10⁻⁵).

TABLE C CCG mean p- Recurrence N Co-variates value* Hazard RatioTRAINING 212 none 0.00404 1.24 (31 CCGs) 204 post-surgery 0.03320 1.16nomogram VALIDATION 199 none 1.8 × 10⁻⁹ 2.68 (26-CCG subset) 197post-surgery 4.8 × 10⁻⁵ 1.94 nomogram *Mean of cell cycle geneexpression with imputation of missing values, likelihood ratio test forCox proportional hazards model.

To help understand the interaction between the nomogram and the CCGexpression signature, a scatter plot comparing these predictors (FIG. 4)was generated (light gray stars represent patients whose cancer recurredwhile black stars represent patients whose cancer did not). Analysis ofthe scatter plot by KM means divided the samples into three clustersbased on nomogram score only. Subsequently, it was discovered that theclusters were based on well-understood clinical parameters. The patientsin the lowest scoring cluster (116/117) had organ-confined disease.Patients in the middle scoring cluster (48/60) had at least onepost-surgical parameter known to be associated with poor outcome (i.e.,disease through the capsule, disease positive lymph nodes, and/ordisease positive seminal vesicles) and low pre-surgical PSA (<10 ng/ml).Patients in the highest scoring cluster had at least one unfavorablepost-surgical parameter and high pre-surgery PSA. Next, the patients inthe low and medium scoring clusters were divided by the mean of the CCGscore. Outcomes for patients in the highest scoring cluster areadequately predicted by the nomogram and, therefore, were not dividedfurther. As a result, the scatter plot defines five patient groups withdisease recurrence rates of 2%, 40% (for two groups), 65%, and 80%(Table D). The recurrence rate of all five groups versus time is shownin FIG. 5.

TABLE D Post-RP nomogram CCG score Low Medium High Low 1/62 (1.6%) 13/31(41.9%) 16/20 (80%) High 21/55 (38.2%) 19/29 (65.5%)

The scatter plot shown in FIG. 4 suggests that there is a non-linearinteraction between the CCG signature and the post-surgical nomogram.That is, the CCG signature is a better predictor in patients with lownomogram scores. Therefore, the study tested for statistical evidence ofan interaction between these variables in a multivariate model forpredicting disease recurrence (Table E). There was significant evidencefor a favorable interaction in both training and validation studies.Including the interaction term in the model dramatically improved theprognostic significance of the CCG signature after adjusting for thenomogram (p-values of 0.0015 in training and 1.2×10⁻⁸ in validationcohort).

TABLE E Statistical Summary Inde- Recur- pendent Co Inter- Vari- rencevari- vari- action able Hazard Cohort N ables ates p-value p-value ratioTraining 204 nomo- none NA 1.6 × 10⁻¹⁰ gram 212 CCG none NA 0.004  1.24signa- ture 204 CCG nomo- 0.021  0.0015 signa- gram ture Valida- 197nomo- none NA 7.7 × 10⁻¹³ tion gram 199 CCG none NA 1.8 × 10⁻⁹  2.68signa- ture 197 CCG nomo- 0.0001 1.28 × 10⁻⁸   signa- gram ture

Example 3

The following study aimed at determining the optimal number of CCGs toinclude in the signature. As mentioned above, CCG expression levels arecorrelated to each other so it was possible that measuring a smallnumber of genes would be sufficient to predict disease outcome. In fact,single CCGs from the 31-gene set in Table 7 (Panel C) add significantlyto the Kattan-Stephenson nomogram, as shown in Table F below (afteradjustment for the nomogram and an interaction term between the nomogramand CCG expression):

TABLE F Gene p- Gene # Symbol value* 1 NUSAP1 2.8E−07 2 DLG7 5.9E−07 3CDC2 6.0E−07 4 FOXM1 1.1E−06 5 MYBL2 1.1E−06 6 CDCA8 3.3E−06 7 CDC203.8E−06 8 RRM2 7.2E−06 9 PTTG 1 1.8E−05 10 CCNB2 5.2E−05 11 HMMR 5.2E−0512 BUB1 8.3E−05 13 PBK 1.2E−04 14 TTK 3.2E−04 15 CDC45L 7.7E−04 16 PRC11.2E−03 17 DTL 1.4E−03 18 CCNB1 1.5E−03 19 TPX2 1.9E−03 20 ZWINT 9.3E−0321 KIF23 1.1E−02 22 TRIP13 1.7E−02 23 KPNA2 2.0E−02 24 UBE2C 2.2E−02 25MELK 2.5E−02 26 CENPA 2.9E−02 27 CKS2 5.7E−02 28 MAD2L1 1.7E−01 29 UBE2S2.0E−01 30 AURKA 4.8E−01 31 TIMELESS 4.8E−01 *p-value for likelihoodratio test of full (post-RP nomogram score + cell cycle expression +nomogram:cell cycle) vs reduced (post-RP nomogram score only) CoxPHmodel of time-to-recurrence.

To evaluate how smaller subsets of the larger CCG set (i.e., smaller CCGpanels) performed, the study also compared how well the signaturepredicted outcome as a function of the number of CCGs included in thesignature (FIG. 1). Time to chemical recurrence after prostate surgerywas regressed on the CCG mean adjusted by the post-RP nomogram score.Data consist of TLDA assays expressed as deltaCT for 199 FFPE prostatetumor samples and 26 CCGs and were analyzed by a CoxPH multivariatemodel. P-values are for the likelihood ratio test of the full model(nomogram+cell cycle mean including interaction) vs the reduced model(nomogram only). As shown in Table G below and FIG. 1, small CCGsignatures (e.g., 2, 3, 4, 5, 6 CCGS, etc.) add significantly to theKattan-Stephenson nomogram:

TABLE G # of Mean of log10 CCGs (p-value)* 1 −3.579 2 −4.279 3 −5.049 4−5.473 5 −5.877 6 −6.228 *For 1000 randomly drawn subsets, size 1through 6, of cell cycle genes.

Example 4

The aim of this experiment was to evaluate the association between PTENmutations and biochemical recurrence in prostate cancer patients afterradical prostatectomy. Somatic mutations in PTEN were found to besignificantly associated with recurrence, and importantly, it addedprognostic information beyond both the established clinical nomogram forprostate cancer recurrence (the Kattan-Stephenson nomogram) and the CCGsignature score (described in Examples 1 & 2, supra).

Patients and Methods

Eight hundred four consecutive RP patients were followed for a median of9.5 years. The patient characteristics and the treatment outcomes of theentire cohort have been previously reported (Swanson et al., UROL.ONCOL. (2007) 25:110-114). Tissue blocks and/or slides from the finalpathological evaluation with enough tissue for analysis were availablefor 430 patients. Of these, 191 were selected for PTEN mutationscreening based on the amount of available tumor.

Genomic DNA was isolated from the FFPE tumor samples for mutationscreening of PTEN using the QIAamp DNA FFPE Tissue kit (Qiagen,Valencia, Calif.) according to the kit protocol. The FFPE slides werefirst stained with hematoxylin and eosin and examined by a pathologistto identify the tumor region. After deparaffinization, tumor tissue wascut out from the slides by a razor blade. For a few samples dissectionwas aided by laser capture microscopy (LCM), owing to the dispersion ofthe tumor cells

Mutations were detected by designing sequencing primers to interrogatethe PTEN genomic sequence. The primers contained M13 forward and reversetails to facilitate sequencing. After amplification, DNA sequence wasdetermined on a Mega BASE 4500 (GE healthcare) using dye-primerchemistry as described in Frank et al., J. CLIN. ONCOL. (2002)20:1480-1490. Due to the technical difficulties associated withsequencing DNA derived from FFPE material, each mutation was detected byat least two independent amplification and sequencing reactions.

Statistical Methods:

Unless otherwise specified, the association between biochemicalrecurrence and PTEN mutations was evaluated using Cox PH models for timeto recurrence. The resultant p-values were derived from a likelihoodratio test comparing the null model to the model containing the testvariable. In this example (Example 4), the CCG signature was derivedfrom 26 CCGs (Panel D in Table 2, supra). All of the expression datawere generated in triplicate. The expression data were combined into asignature by calculating the mean expression level for 26 CCGs. Theclinical data were the variables included in the Kattan-Stephensonnomogram.

Results

PTEN mutations were found in 13 individuals (13/191). In this subset of191 patients, PTEN was a significant predictor of biochemical recurrence(p-value=0.031). The recurrence rate in mutation carriers was 69% (9/13)compared to 36% (64/178) in non-mutant patients. The difference inrecurrence rate is also significant using a Fisher's exact test(p-value=0.034). In the subset of patients with clinical parameter data,CCG signature score, and PTEN mutations, PTEN status was a significantpredictor of biochemical recurrence after adjusting for both clinicalparameters and CCG signature (p-value 0.024). Finally, the combinationof PTEN mutation with CCG signature was a better predictor of outcomeafter adjusting for clinical parameters than using the CCG signatureafter adjusting for clinical parameters (p-value=0.0002 for thecombination compared to 0.0028 for CCG only). These results show thatPTEN mutations provide information about the likelihood of recurrencethat is uncorrelated with either clinical parameters or CCG signature,and that using all three parameters to evaluate recurrence risk providesa more accurate estimate of recurrence probability than previouslypossible.

Example 5

This Example describes further studies to validate and refine someembodiments of the CCG signatures of the disclosure.

Patients and Methods

Eight hundred four consecutive radical prostatectomy patients werefollowed for a median of 9.5 years. The median age was 67 years. Theclinical stage was T1 34%, T2 66% and T3<1%. The median preoperative PSAwas 6.6 ng/ml with 72%<10 ng/ml and 28%>10 ng/ml. The specimens wereinked and clinical parameters were recorded as to positive bladder neckor urethral margin, invasion into the capsule, extension through thecapsule, positive margins and the involvement of the seminal vesicles.Biochemical recurrence was defined as a PSA>0.3 ng/ml. For this study wehad access to clinical data on 690 patients. Tissue blocks and/or slidesfrom the final pathological evaluation with enough tissue for analysiswere available for 442 patients. The cohort was divided into 195patients for a training cohort, and 247 patients for validation.

Selection of Genes

Assays of 126 CCGs and 47 HK (housekeeping) genes were run against 96commercially obtained, anonymous prostate tumor FFPE samples withoutoutcome or other clinical data. The working hypothesis was that theassays would measure with varying degrees of accuracy the sameunderlying phenomenon (cell cycle proliferation within the tumor for theCCGs, and sample concentration for the HK genes). Assays were ranked bythe Pearson's correlation coefficient between the individual gene andthe mean of all the candidate genes, that being the best availableestimate of biological activity. Results for the correlation of each ofthe 126 CCGs to the mean are reported in Table 23. Not including CCGswith low average expression, or assays that produced sample failures,approximately half the CCGs had correlations less than 0.58, and aquarter of the HK genes had correlations less than 0.95. These assayswere eliminated, leaving a subset of 56 CCGs (Panel G) and 36 HKcandidate genes (Tables 11 and 12). Correlation coefficients wererecalculated on this subset, and the final selection was made from theranked list.

Gene Expression

Total RNA was extracted from representative 5 μM thick FFPE tumorsections. The samples were de-paraffinized using a xylene bath andsubsequently hydrated in graded series of ethanol baths. Afterward, thetumor region was dissected from the slide using a razor blade accordingto the pathologist instructions. Alternatively, the tumor region wasdissected directly into an eppendorf tube and the paraffin was removedusing xylene and washed with ethanol. After, samples were treatedovernight with proteinase K digestion at 55° C. Total RNA was extractedusing either RNeasy FFPE or miRNeasy (Qiagen) as described by themanufacturer (with the only exception being the extended proteinase Kdigestion described above). Isolated total RNA was treated with DNase I(Sigma) prior to cDNA synthesis. Subsequently, we employed theHigh-capacity cDNA Archive Kit (Applied Biosystems) to convert total RNAinto single strand cDNA as described by the manufacturer. A minimum of200 ng RNA was required for the RT reaction.

Prior to measuring expression levels, the cDNA was pre-amplified with apooled reaction containing TaqMan™ assays. Pre-amplification reactionconditions were: 14 cycles of 95° C. for 15 sec and 60° C. for 4minutes. The first cycle was modified to include a 10 minute incubationat 95° C. The amplification reaction was diluted 1:20 using the 1×TEbuffer prior to loading on TaqMan™ Low Density Arrays (TLDA, AppliedBiosystems) to measure gene expression.

CCG score

The CCG score is calculated from RNA expression of 31 CCGs (Panel F)normalized by 15 housekeeper genes (HK). The relative numbers of CCGs(31) and HK genes (15) were optimized in order to minimize the varianceof the CCG score. The CCG score is the unweighted mean of CT values forCCG expression, normalized by the unweighted mean of the HK genes sothat higher values indicate higher expression. One unit is equivalent toa two-fold change in expression. Missing values were imputed using themean expression for each gene determined in the training set using onlygood quality samples. The CCG scores were centered by the mean value,again determined in the training set.

A dilution experiment was performed on four of the commercial prostatesamples to estimate the measurement error of the CCG score (se=0.10) andthe effect of missing values. It was found that the CCG score remainedstable as concentration decreased to the point of 5 failures out of thetotal 31 CCGs. Based on this result, samples with more than 4 missingvalues were not assigned a CCG score.

The CCG score threshold for determining low-risk was based on the lowestCCG score of recurrences in the training set. The threshold was thenadjusted downward by 1 standard deviation in order to optimize thenegative predictive value of the test.

Model of Clinical Risk

A Cox proportional hazards model was used to summarize the availableclinical parameter data and estimate the prior clinical risk ofbiochemical recurrence for each patient. The data set consisted of 195cases from the training set and 248 other cases with clinical parameterinformation but insufficient sample to measure RNA expression.Univariate tests were performed on clinical parameters known to beassociated with outcome (see Table H below). Non-significant parameterswere excluded from the model. A composite variable was created fororgan-confined disease, with invasion defined as surgical margins,extracapsular extension, or involvement of any of seminal vesicles,bladder neck/urethral margins, or lymph nodes. The composite variablefor organ-confined disease proved more significant in the model than anyof its five components, some of which were inter-correlated or notprevalent. Model fitting was performed using the AIC criteria forpost-operative covariates.

TABLE H Univariate analysis of clinical parameters and association withbiochemical recurrence Cinical Variable p-value* # occurrences TotalFrequency BLADDER 0.0002  36 443 0.081 CAPSULAR 1.1 × 10⁻⁹  194 4430.438 ETHNICITY 0.6741 416 439 0.948 (WHITE) LYMPHNOD 0.0009  33 4430.074 MARG.POS 6.1 × 10⁻¹¹  83 443 0.187 PATHGLEA 6.7 × 10⁻¹⁶ NA 443 NAPATHGRAD 2.4 × 10⁻¹¹ NA 443 NA PATHSTAG 3.1 × 10⁻¹⁵ NA 443 NAPRE.PSA.LOG10 6.2 × 10⁻¹² NA 443 NA SEM.VES 3.0 × 10⁻⁸   56 443 0.126SURGERY.YEAR 0.0803 NA 443 NA THRU.CAP 1.3 × 10⁻¹⁰ 114 443 0.257 *Cox PHp-value for likelihood ratio test

The final model (i.e., nomogram) has binary variables for organ-confineddisease and Gleason score less than or equal to 6, and a continuousvariable for logarithmic PSA (Table I). This model includes all of theclinical parameters incorporated in the post-RP nomogram (i.e.,Kattan-Stephenson nomogram) except for Year of RP and the two componentsof the Gleason score. The distribution of prior clinical risk showsthree distinct nodes (FIG. 8). K-means clustering with 3 centers wasused to set the threshold for the low-risk cluster, which comprisesapproximately 50% of the sample.

TABLE I Clinical Model Clinical Parameter Coefficient HR p-value*organ-confined disease −0.827 0.44 3.4 × 10⁻⁶ Gleason score ≤6 −0.87340.42 4.2 × 10⁻⁷ log PSA 0.6678 1.95 2.0 × 10⁻⁴ *Cox PH p-value forlikelihood ratio testStatistical Analysis

Clinical parameters were compared between the training and validationsets using the Student's t-test for continuous parameters and Fisher'sexact test for categorical parameters. The prior clinical risk ofpatients for biochemical recurrence after surgery was estimated by apost-RP nomogram score summarizing 7 covariates. K-means clustering ofthe nomogram score was used to categorize patients as low or high priorclinical risk. Expression data were expressed as the CT (the PCR cycleat which the fluorescence intensity exceeds a predetermined threshold)of each CCG normalized by the mean of the 15 housekeeper genes (Table 12above).

Poor quality samples were excluded from analysis to eliminate poorquality samples or dubious readings without compromising the integrityof the signature by inadvertently excluding samples with low CCGexpression. Accordingly, the thresholds for cleaning or filtering thedata were set conservatively. Mean expression levels of the HK genes foreach sample, which were higher than those of the CCGs, were used toidentify poor quality samples. Technical metrics for the amplificationefficiency and excessively high standard deviations of replicates wereused to identify unreliable CT measurements. No failures of HK genes,and no more than 1 failure out of 3 replicates for CCGs, were allowed.

The association between biochemical recurrence and CCG expression afteradjusting for clinical risk predicted by clinical parameters wasevaluated using a Cox proportional hazards model for time-to-recurrence.The proportional hazards assumption of no time-dependence was tested forthe full model of the CCG signature plus the binary clinical parameterscore with an interaction term, and for the CCG signature only in theclinical risk subsets. It was not significant in either training orvalidation, indicating that there is no evidence for time-dependence.All of the p-values reported are from a likelihood ratio test comparingthe reduced or null model to the model containing the test variable.Kaplan-Meier plots are used to show estimated survival probabilities forsubsets of patients; however, p-values are from the Cox likelihood ratiotest for the continuous values of the variable. All statistical analyseswere performed in S+ Version 8.1.1 for Linux (TIBCO Spotfire) or R 2.9.0(http://www.r-project.org).

Results

We isolated RNA from FFPE tumor sections derived from 442 prostatecancer patients treated with RP. The cohort was split into 195 patientsfor initial characterization of the signature (“training set”) and 247patients for validation. The clinical parameters of the training andvalidation cohort are listed in Table J. There were no significantdifferences after adjusting for multiple comparisons.

TABLE J Clinical parameters of training and validation patient cohortsStatistical Clinical Parameter Training Validation p-value Analysis Agein years 67.5 66.8 0.204 t-test at RP, mean (sd) (6.2) (5.6) Ethnicity3.10% 7.30% 0.058 Fisher's (% non-white) exact (2 Black, 3 (10 Black, 7Hispanic, 1 Hispanic, 1 other) other) Recurrence 73/195 90/247 0.843Fisher's (37.4%) (36.4%) exact Days to recurrence, 839 736 0.308 t-testmedian Days to follow-up, 3300 3332 0.556 t-test median Pre-RP surgeryPSA, 7.4 6.4 0.022 t-test of median log Seminal vesicles 23/195 33/2470.668 Fisher's (11.8%) (13.4%) exact Bladder neck/urethral 12/195 16/2471 Fisher's margin (6.2%) (6.5%) exact Lymph nodes 8/195 12/247 0.819Fisher's (4.1%) (4.9%) exact Capsular penetration 104/195 115/247 0.18Fisher's (53.3%) (46.6%) exact Through the capsule 66/195 73/247 0.354Fisher's (33.8%) (29.6%) exact Positive margins 51/195 61/247 0.742Fisher's (26.2%) (24.7%) exact Post-RP Gleason 114/195 166/247 0.06Fisher's score < 7 (58.5%) (67.2%) exact Organ-confined 108/195 156/2470.118 Fisher's disease (55.4%) (63.2%) exact 10-year PFP 61% (52%, 67%(60%, 0.905 Log-rank (95% CI) 69%) 73%) test

To analyze the CCG signature for this study, we tested 126 CCGs on RNAderived from 96 prostate tumors (Table 11). The tumor samples wereanonymous and not associated with clinical data. From this set of genes,we selected 31 genes (Panel F) for inclusion in our signature (Table K).The genes were selected based on their technical performance, and by howwell each gene correlated with the mean expression level of the entireCCG set, in the 96 anonymous samples.

TABLE K CCG Signature from Training Set (Panel F) Symbol GeneID ASF1B55723 ASPM 259266 BIRC5 332 BUB1B 701 C18orf24 220134 CDC2 983 CDC20 991CDCA3 83461 CDCA8 55143 CDKN3 1033 CENPF 1063 CENPM 79019 CEP55 55165DLGAP5 9787 DTL 51514 FOXM1 2305 KIAA0101 9768 KIF11 3832 KIF20A 10112MCM10 55388 NUSAP1 51203 ORC6L 23594 PBK 55872 PLK1 5347 PRC1 9055 PTTG19232 RAD51 5888 RAD54L 8438 RRM2 6241 TK1 7083 TOP2A 7153

To evaluate the prognostic utility of the CCG signature, we generatedexpression data on 195 patients in the training set. Since theindividual gene expression levels were correlated, we combined them intoa signature score by calculating the mean expression for the entire setof 31 genes (Panel F), normalized by 15 housekeepers (Table 12). The CCGscore distribution was centered at zero, and each score unit correspondsto a 2-fold change in expression level. Poor quality samples wereidentified by observing either low expression of housekeeping genes oran unacceptable number of CCG failures, and excluded from the analysis.After applying our exclusion rules, there were 140 samples available foranalysis. Association between biochemical recurrence and CCG expressionwas evaluated using Cox PH models for time to recurrence. A high CCGexpression value was predictive of disease recurrence in a univariateanalysis (p-value=0.01, Table 17).

Next, we evaluated the prognostic utility of the CCG signature afteraccounting for clinical parameters known to be associated withrecurrence after RP. To account for clinical measures in our analysis,we created a model/nomogram that included preoperative PSA, Gleasonscore, and evidence of disease outside the prostate (i.e., any of eitherextracapsular extension, or positive post-surgical pathology on lymphnodes, margins, bladder neck, urethral margin or seminal vesicles). Themodel was optimized in 443 patients (Tables 13 & 14), including allpatients for whom we had clinical data but were not in the validationset, and was a highly significant predictor of recurrence in thetraining cohort (p-value=2.5×10⁻¹¹). The distribution of the scores fromthe clinical model contained several modes (FIG. 8), separating high-and low-risk patient groups. Therefore, the score was used subsequentlyas a binary variable (high or low risk). The low-risk cluster correlatedwith a consistent set of clinical parameters. Specifically, the vastmajority (215/218) had organ-confined disease and Gleason score <7. Inaddition, 80% had low pre-surgical PSA (<10 ng/ml). Patients in thehigh-risk cluster (N=225) were more heterogeneous, but tended to haveclinical characteristics known to be associated with poor outcome (e.g.,Gleason>6 and/or disease through the capsule).

Multivariate analysis of the training set incorporating our binaryclinical model, showed evidence for a non-linear interaction between theexpression signature and clinical parameters (Table L). To help usunderstand the nature of this interaction, we generated a scatter plotcomparing these predictors (FIG. 8). As evident from the figure, the CCGscore proved useful for evaluating recurrence risk in patients definedas low risk by clinical parameters. In fact, even after adjusting forthe clinical model within the low risk patients, the CCG signature was astrong predictor of biochemical recurrence (p-value=0.0071).

TABLE L Statistical Summary Subset based 31-gene training N = 19531-gene validation N = 247 on clin. Main effect Interaction Main effectInteraction model p-value p-value n p-value p-value n CCG score 0.01 1405.8 × 10⁻⁸ 218 Binary clin. 5.1 × 10⁻⁶ 133  1.1 × 10⁻¹⁰ 215 risk (low vshigh) CCG score 0.018 0.032 133 8.3 × 10⁻⁷ 0.026 215 adjusted for binaryclin. risk + interaction CCG score low-risk 0.0038 54 7.5 × 10⁻⁵ 112only Clin. risk low-risk 0.22 54 0.044  112 score CCG score low-risk0.0071 54  0.00019 112 adjusted for clin. risk (clin. risk vs clin.risk + CCG) CCG score high-risk 0.48 79 5.8 × 10⁻⁴ 103 Clin. riskhigh-risk 2.8 × 10⁻⁶ 79 0.0076 103 score CCG score high-risk 0.51 790.0026 103 adjusted for clin. risk (clin. risk vs clin. risk + CCG)

We used our training data in the scatter plot to establish an optimizedthreshold score of −0.16 for the CCG signature (the mean CCG score iszero). FIG. 12 shows this threshold applied to the 443 patients studiedin this example. Forty percent of low-risk patients fall below thisthreshold, and it was selected so that there were no recurrences10-years after RP (i.e., negative predictive value (NPV) of 100%). As aresult of establishing threshold values for both the clinical model andCCG score, the scatter plot was divided into four sections withrecurrence rates of 0% (low CCG) and 26% (high CCG) for low-riskpatients; and 60% (low CCG) and 50% for high-risk patients.

Next, we generated CCG expression data on 247 patients in our validationcohort. Thirty-two samples were eliminated from further analysisaccording to the exclusion rules developed on the training cohort. PanelF was a significant predictor of biochemical recurrence in a univariateanalysis (p-value=5.8×10⁻⁸, Table L). After adjusting for the binaryclinical model, the CCG signature was highly predictive of recurrence inthe validation cohort (p-value 8.3×10⁻⁷), and as in the training set,there was significant evidence for a non-linear interaction betweenvariables. The CCG signature was informative across the entire spectrumof clinically defined risk (Table 17). In terms of validating thetraining results, the p-value for association between recurrence and CCGsignature in low-risk patients was 1.9×10⁻⁴.

We applied the CCG threshold derived from our analysis of the trainingcohort to our validation data set (FIG. 9). Low risk patients with CCGscores below the threshold had a 10-year predicted recurrence rate of 5%(equivalent to validated NPV of 0.95). Overall, the combination of CCGscore and clinical parameters divided the cohort into four groups with10 year predicted recurrence rates of 5%, 22%, 36% and 70% (Table M).The predicted recurrence rate versus CCG score for patients in thevalidation cohort is shown in FIGS. 10 & 11.

TABLE M Summary of recurrence rates in validation cohort defined byclinical risk and CCG score 10-year recurrence rate Clinical CCGKaplan-Meier risk score estimate n low low 0.05 39 low high 0.22 73 highlow 0.36 27 high high 0.7 76

We tested our validated threshold versus various definitions of low-riskpatients (Table N). The signature score was a significant prognosticindicator in a variety of low-risk clinical definitions, and dependingon definition, generated a 10-year predicted recurrence rate of 0.05 to0.10.

TABLE N NPV of CCG signature in other definitions of low-risk patientslow CCP* 10-yr predicted Clinical definition of low risk recurrence** np-value*** Organ-confined disease and Gleason 0.05 39 9.4 × 10⁻⁴ score <7 & PSA < 10 Organ-confined disease and Gleason 0.08 40 5.8 × 10⁻³ score< 7 Organ-confined disease and Gleason 0.07 42 8.7 × 10⁻⁴ score < 8 &PSA < 10 Organ-confined disease and Gleason 0.1 43 4.1 × 10⁻³ score < 8Organ-confined disease only 0.1 44 2.4 × 10⁻³ *defined by validatedthreshold **Kaplan-Meier estimates ***for difference between KMestimates for low and high risk adjusted by Greenwood variance.Comment

We have developed and validated a prognostic molecular signature forprostate cancer. The signature is based on measuring mRNA expressionlevels of cell cycle genes (CCGs). By definition, expression of CCGs isregulated as a function of cell cycle stage. That is, they are turned onat specific cell cycle stages, so that actively growing cells havehigher expression levels of CCG than quiescent cells. Presumably thisfact underlies the signature's ability to predict cancer progression.Without wishing to be bound by theory, it is thought that by measuringthe expression levels of CCG we are indirectly measuring the growth rateand inherent aggressiveness of the tumor, which ultimately impacts onthe likelihood of prostate cancer recurrence after prostatectomy.

There is an important distinction between this study and many othersthat have attempted to generate prognostic molecular signatures. Often,similar studies begin with a very large number of candidate biomarkers(sometimes exceeding 1000's of genes) that are then evaluated forassociation with a clinical phenotype of interest. This approach may attimes suffer from inherent multiple testing which can make thesignificance of the derived signature uncertain. Here we have tested asingle hypothesis: CCG would be prognostic in prostate cancer (in factwe selected genes based on their correlation with CCG expression, notbased on association with recurrence). And since CCG expression iscorrelated, we combined the expression data into a predictive signatureby determining the mean expression value of all the genes in thesignature. The simplicity of this approach, biologically andcomputationally, supports the view that the central claim of this studyis likely to be highly robust, and replicated in subsequent studies.

The CCG signature (Panel F) is independently predictive and addssignificantly to the predictive power of the clinical parameterstypically employed to predict disease recurrence after surgery. This istrue in both our training and validation cohorts.

The signature is immediately useful for defining the risk of patientswho present with low-risk clinical parameters. Here, we essentiallydefined low-risk as Gleason<7, PSA<10 and organ-confined disease. TheCCG signature score effectively subdivides the low-risk group intopatients with very low recurrence rates (5%), and a higher risk ofrecurrence (22%) (FIG. 9 & Table M). This is the most dramatic effect ofthe molecular signature—accurately redefining the risk of patientspreviously defined as low-risk based on clinical parameters. It isnoteworthy that within this patient subpopulation (i.e., patientsdefined as low-risk based on clinical parameters) clinical parametersare not particularly prognostic (see Table L). Therefore as a diagnostictest, the signature could be useful for a large number of patients. Inthis study, nearly 60% of the cohort was characterized as low-risk and40% of those are expected to have low CCG scores. Therefore, the CCGsignature can predict indolent disease in a quarter of the patients whohave previously been identified as high-risk (and therefore identifiedas candidates for radical prostatectomy). Finally, the validation datain particular suggests that the CCG signature may be useful for definingrisk in all patients. Specifically, it helped to divide patients definedas high-risk according to clinical parameters into those with 30% and70% recurrence rates (Table M).

The combination of clinical parameters and CCG signature enablesphysicians to more accurately predict risk of surgical failure, andtherefore, identify the appropriate course of therapeutic intervention.As we have shown, the signature dramatically improves the recurrenceprediction for patients who present with general clinical parameters ofnon-aggressive disease (Table N). Within this clinical subgroup,patients with low CCG scores would benefit from the absolute reassurancethat no further treatment is indicated. Conversely, the high CCG groupmay warrant immediate intervention. Patients with unfavorablepost-surgical clinical parameters benefit from adjuvant radiationtherapy. Therefore the CCG signature should predict the efficacy ofadjuvant radiation for patients with low-risk clinical characteristicsand high CCG scores. In the validation cohort, patients with high CCGscores and disease beyond the prostate have a recurrence rate of 70%,which should clearly identify patients who are good candidates foradjuvant radiation. Thus the combination of clinical parameters and CCGsignature clearly leads to more accurately defined patient risk, whichshould enable a more intelligent assessment of the need for furthertreatment.

Example 6

Some of the CCGs panels described herein were further evaluated fortheir ability to prognose additional cancers. Panels C, D, and F werefound to be prognostic to varying degrees in bladder, brain, breast, andlung cancer.

Methods

Gene expression and patient data was obtained from the followingpublicly available datasets: GSE7390 (Desmedt et al., CLIN. CANCER RES.(2007) 13:3207-14; PMID 17545524); GSE11121 (Schmidt et al., CANCER RES.(2008) 68:5405-13; PMID 18593943); GSE8894 (Son et al.; no publication);Shedden (Shedden et al., NATURE MED. (2008) 14:822; PMID 18641660);GSE4412 (Freije et al., CANCER RES. (2004) 64:6503-10; PMID 15374961);GSE4271 (Phillips et al., CANCER CELL (2006) 9:157-73; PMID 16530701);GSE5287 (Als et al., CLIN. CANCER RES. (2007) 13:4407-14; PMID17671123). Each of these datasets has an associated detailed descriptionof the experimental procedures used in gathering expression and patientdata. The expression microarrays used to generate each dataset aresummarized below in Table O.

TABLE O Dataset Array GSE7390 Affymetrix U133 A GSE11121 Affymetrix U133A GSE8894 Affymetrix U133 plus 2.0 Shedden Affymetrix U133 A GSE4412Affymetrix U133 A and B GSE4271 Affymetrix U133 A and B GSE5287Affymetrix U133 A

Expression data for each of the genes in Panels C, D and F was gatheredfrom these datasets and the mean expression level for each Panel wasdetermined for each patient, whose clinical outcome was known (e.g.,recurrence, progression, progression-free survival, overall survival,etc.). CCG score is an average expression of the genes in a panel. If agene is represented by more than one probe set on the array, the geneexpression is an average expression of all the probe sets representingthe gene. The association between CCG score and survival or diseaserecurrence was tested using univariate and multivariate Cox proportionalhazard model. Multivariate analysis was performed when relevant clinicalparameters (grade in brain cancer, stage in lung cancer, NPI in breastcancer) were available.

Results

As shown in Table P below, each Panel, in univariate analysis, was aprognostic factor in each of the cancers analyzed.

TABLE P p-value Cancer Type Dataset Panel C Panel F Panel B ER positivebreast cancer GSE7390 2.4 × 10⁻³ 2.3 × 10⁻³ 4.3 × 10⁻³ ER positivebreast cancer GSE11121 1.2 × 10⁻⁵ 8.7 × 10⁻⁶ 1.5 × 10⁻⁵ Lungadenocarcinoma GSE8894 2.0 × 10⁻³ 2.5 × 10⁻³ 5.6 × 10⁻³ Lungadenocarcinoma Shedden 1.3 × 10⁻⁷ 2.6 × 10⁻⁷ 2.2 × 10⁻⁷ Brain cancerGSE4412 3.2 × 10⁻⁵ 2.2 × 10⁻⁵ 9.0 × 10⁻⁵ Brain cancer GSE4271 1.3 × 10⁻³1.0 × 10⁻³ 2.8 × 10⁻⁴ Bladder cancer GSE5287 6.4 × 10⁻² 5.0 × 10⁻² 8.6 ×10⁻²

As shown in Table Q below, each Panel was also prognostic inmultivariate analysis when combined with at least one clinical parameter(or nomogram).

TABLE Q p-value Additional Clinical Cancer Type Dataset Panel C Panel FPanel B Variable/Nomogram Brain cancer GSE4271 0.022  0.017  0.0065grade Lung Shedden 1 × 10⁻⁶ 2.1 × 10⁻⁶ 1.4 × 10⁻⁶ stage adenocarcinomaER positive breast GSE7390 0.0077 0.0064 0.011  Nottingham cancerPrognostic Index (NPI) ER positive breast GSE11121 0.0041 0.0027 0.0045NPI cancer

Example 7

For the present experiment, cases were defined as men who died fromprostate cancer within 5 years. Controls were defined as men who livedfor at least 10 years. Next, cases and controls were rank ordered bycombined score (as discussed in paragraphs [0066]-[0068] above). Thedistribution of cases and controls by combined score is given in FIG.18.

We selected 25 cases with the lowest combined scores and 31 controlswith the highest combined scores for expression analysis of thetranscriptome using Illumina™ Hi-Seq 2000™. RNA isolation and libraryconstruction were done according to the manufacture's protocol.

Statistical Analysis

RNA expression is measured for all transcript products (TP). Raw countswere normalized by the 75^(th) percentile of all TP's for each sampleand run, then converted to the base 2 logarithm. Multiple TP's for thesame gene locus are combined into a unified gene (UG).

RNA expression data for each sample were compiled from the TP's for theset of loci with single TP's, and UG's from the set of loci withmultiple TP's. In order to be able to include transcripts with zerocounts, we used the base 2 logarithm of the normalized counts+1 for theanalysis.

The primary analysis was designed to find associations between RNAexpression and case-control status. Kolmogorov-Smirnov tests wereperformed at each locus, and the results were ranked by p-value. Inaddition, each of the candidate genes was tested in a logisticregression model including CCP score, serum PSA, and Gleason.

Results

Based on the analysis of the whole transcriptome, we identified sixcandidate genes (Table R) as being associated with prostate cancer deathafter adjustment for CCP score and clinical parameters. All of thesegenes had a p-value of less than 0.001 in the multivariate model. Thedistribution of observed p-values compared to the expected (given noassociation) is given in FIG. 19. Some p-values were more significantlyassociated with prostate cancer death than expected by chance.

TABLE R Panel H Gene Gene Gene # Symbol ID p-value 1 KLK3 354  2 × 10⁻⁶2 STX4 6810 1.7 × 10⁻⁵ 3 TAF5L 27097 3.3 × 10⁻⁵ 4 GTPB5 26164 5.2 × 10⁻⁵5 SIRT3 23410 9.7 × 10⁻⁵ 6 EIF3D 8664 1.97 × 10⁻⁴ 

With slightly different parameters, the following genes were identifiedas the best predictors (FIG. 5):

TABLE S Panel H Gene # Gene Symbol Gene ID p-value 1 KLK3 354 1.7 × 10⁻⁵2 GTPBP5 26164 1.4 × 10⁻⁴ 3 LOC100126784 100126784 2.2 × 10⁻⁴ 4 ABCG19619 3.93 × 10⁻⁴  5 CYP1B1-AS1 1545 3.96 × 10⁻⁴  6 CECR6 27439 4.8 ×10⁻⁴

The RNA expression profiles underlying the significant p-values aregiven in FIGS. 20 & 22. The highest ranked gene was KLK3. Low levels ofKLK3 RNA were associated with poor prognosis. KLK3 RNA expression levelswere uncorrelated with serum PSA (Pearson correlation coefficient withlog of serum PSA=0.13, p-value=0.33). KLK3 RNA expression predicts casecontrol status independently of Gleason (FIG. 21).

Example 8

Panel F was combined with certain clinical features and/or clinical riskstratifiers and the combination(s) was shown to predict risk of prostatecancer-specific death in biopsy samples.

Patients and Samples

Samples were analyzed using the process described in the precedingExamples (in some cases data was used from the actual sample analysisdescribed in the preceding Examples). Data from prostate cancer patientsamples were combined from six different cohorts, designated P1, P2, P3,P4, P5A, P5B, and P7 (P5A and P5B were distinguishable subsets (radicalprostatectomy v. radiation) of a larger P5 cohort). Characteristics ofthese cohorts are given in Table T.

TABLE T Cohort Patients Patients Sample Outcome # Clinical Total TypeTreatment Measure P1 200 337 TURP conservative death from (activeprostate surveillance) cancer P2 180 349 needle conservative death frombiopsy (active prostate surveillance) cancer P3 353 353 surgical radicalbiochemical tumor prostatectomy recurrence P4 388 413 surgical radicalbiochemical tumor prostatectomy recurrence P5A 131 179 needle radicalbiochemical biopsy prostatectomy recurrence P5B 118 142 needle radiationbiochemical biopsy recurrence P7 272 281 needle unknown unknown biopsy

Patients were only included if they had all the clinical informationrequired to calculate the CAPRA score. Patients who could be assigned toan AUA risk category but who did not have a CAPRA score were alsoexcluded from any analysis. Time-to-event data were censored at 10 yearsin all cohorts. Inception was date of diagnosis for patients with TURPand needle biopsy samples, and date of surgery for patients withsurgical tumor samples. Times were recorded as days for all studiesexcept P1, P5A & P5B, which were in months, and converted to days by afactor of 365.25/12. For patients whose clinical stage did not includethe substage, the following conversions were made: T1 to T1A, T2 to T2A,and T3 to T3A.

Three different subsets were defined to train the Combined score(Training), validate the Combined score and estimate risk of prostatecancer death (Validation), and characterize the distribution of the CCPscore in the US clinical population (US clinical). These are presentedin Table U.

TABLE U Training Validation US clinical P1 P2 P3 P3 P4 P4 P5A P5B P5B P7N = 1059 N = 180 N = 1219AUA Risk Stratification

The AUA nomogram/guideline stratifies the risk of PSA failure andprostate cancer-specific mortality following radical prostatectomy,external beam radiotherapy, or interstitial prostate brachytherapy. SeeAmerican Urological Association, Guideline for the Management ofClinically Localized Prostate Cancer: 2007 Update (available at AUAwebsite). Each patient's risk category was determined according toguidelines interpreted below (AUA Guidelines 2007, page 10). Individualswith clinical stage T1A or T1B, or clinical stage T3, were assigned torisk categories even though the AUA guidelines are technically notapplicable at these stages.

-   -   Low: PSA≤10 ng/mL AND Gleason score≤6 AND clinical stage≤T2A    -   Intermediate: (PSA>10 and ≤20 ng/mL OR Gleason score=7 OR        clinical stage=T2B) AND not qualifying for High Risk    -   High: PSA>20 ng/mL OR Gleason score>7 OR clinical stage≥T2C        CAPRA Nomogram

CAPRA is a preoperative predictor of disease recurrence after radicalprostatectomy. See Cooperberg et al., J. UROL. (2005) 173:1938-1942. Thescores (0 to 10) were calculated according to a point system,interpreted below (see Cooperberg et al. at Table 1). Patients withclinical stage T3B or higher were assigned a score although technicallythe scoring system did not apply. Patients with PSA≤2 ng/mL wereincluded in the lowest interval, which is (2, 6] in Cooperberg et al.Clinical stage and Gleason grades were used instead of pathological datain the post-prostatectomy cohorts, although the CCP score was from asample of the surgical tumor instead of a biopsy.

PSA (ng/mL) 0 [0, 6] 1 (6, 10] 2 (10, 20] 3 (20, 30] 4 (30, 100]Excluded patients with PSA > 100 as per study inclusion criteria.Clinical stage 0 T1/T2 1 ≥ T3A Percent positive cores 0 < 34% 1 ≥ 34%Gleason score 0 Primary 1-3; Secondary 1-3 1 Primary 1-3; Secondary 4-53 Primary 4-5; Secondary 1-5 Gleason score for patients with componentgrades 0 Gleason < 7 1 Gleason 7 3 Gleason > 7 Age at diagnosis 0 < 50years 1 ≥ 50 yearsDeveloping the Combined Score

The Combined score was fit in the training set by a Cox ProportionalHazards model stratified by cohort. Cohort stratification adjusted forthe differences in survival profiles that might be produced by varioustreatment regimens and endpoints in each cohort. CAPRA was treated as aninteger-valued variable (0-10), and CCP score as a continuous numericvariable. To assure that CAPRA was an approximately linear predictor, wetested the quadratic term. It was significant (X²=8; p-value=0.0041),but minor in comparison to the linear term (X²=53, p-value<10⁻¹²).

Interactions with cohort were tested in a preliminary model to confirmthat the prognostication of CAPRA and CCP score was not dependent oncohort. The interaction had a p-value of 0.059 with CAPRA; and a p-valueof 0.050 with CCP score, and was not included in the final model (TableV).

TABLE V Variable Coefficient HR (95% CI) X² (1df) p-value CAPRA 0.3941.48 (1.38, 1.59) 116 <10⁻²⁶ CCP score 0.567 1.76 (1.51, 2.05) 48 <10⁻¹¹

Based on this model, the Combined score was defined asCombined Score=0.39*CAPRA+0.57*CCP scoreValidating the Combined Score

The Combined score was validated in P2, a needle biopsy cohort ofconservatively managed (active surveillance/watchful waiting) patientswith death from prostate cancer as the outcome (Table W). There were 33(18%) deaths among the 180 patients. In a multivariate model where CAPRAwas added to the Combined score, the p-value for the Combined score was0.0028, and the p-value for CAPRA was 0.58, confirming that the Combinedscore adequately accounted for both CAPRA and CCP score in thevalidation cohort.

TABLE W Variable Coefficient HR (95% CI) X² (1df) p-value Combined score0.82 2.27 (1.63, 3.16) 28 <10⁻⁶ CAPRA 0.35 1.42 (1.20, 1.68) 19 <10⁻⁴CCP score 0.75 2.12 (1.49, 3.03) 18 <10⁻⁴Predicting Mortality Risk

The predicted risk of prostate cancer death within 10 years of diagnosiswas estimated in the P2 validation cohort. Times were censored at 10years (120 months) and the predicted risk was estimated at the time ofthe last event (118.1109 months). The range of CCP scores in thevalidation set (n=180) was −0.8 to 4.1. Sample mortality risks are shownin paragraphs [00186] and [00197] above.

Restratifying AUA Risk Based on CCP Score or Combined Score

The percentile corresponding to each 0.1 increment of the CCP score wasdetermined for the US clinical samples from each cohort within each AUArisk category. Individuals with clinical stages of T3 were excluded,leaving 1219 (97%) of the available 1262. The percentile for eachpatient was the fraction of patients within that AUA risk category whohad a lower CCP score. Where multiple patients shared the same CCPscore, rounded to a tenth, the percentile would be the same; namely, thefraction of patients with CCP scores lower than the rounded score.

The median CCP score of the US clinical samples from each cohort withineach AUA risk category was used to assess cancer aggressiveness, asdescribed in the following section. We compared the CCP score of eachindividual to the average CCP score of patients in the same AUA riskcategory in order to offer a relative assessment of canceraggressiveness and in order to modify or confirm the risk predictiongiven using AUA guidelines.

The scale of CCP scores for each AUA risk category consisted of five1-unit intervals, with the middle interval being centered at the medianCCP score for that category in our sample cohort. There wasapproximately a 2-fold change in risk between intervals, which was thehazard ratio corresponding to a 1-unit change in the CCP score. We havegiven each section a qualitative label (Table X).

TABLE X CCP Range and CCP Classification Relative to AUA CategoryConsiderably Considerably Less Aggressive Less Aggressive ConsistentMore Aggressive More Aggressive AUA Risk Low [−2.7, −1.7] (−1.7, −0.7](−0.7, 0.3) [0.3, 1.3) [1.3, 2.3] Category Intermediate [−2.6, −1.6](−1.6, −0.6] (−0.6, 0.4) [0.4, 1.4) [1.4, 2.4] High [−2.5, −1.5] (−1.5,−0.5] (−0.5, 0.5) [0.5, 1.5) [1.5, 2.5]

Example 9

The prognostic utility of CCP genes (in this case, Panel F) and variouscandidate genes including KLK3, all using assay techniques as discussedabove, was evaluated.

Patients

The patients whose samples were used in this experiment wereincidentally diagnosed with prostate cancer after undergoing TURP andmanaged conservatively. The cohort has been described previously (in theExamples above and in Cuzick et al., Long-term outcome among men withconservatively treated localised prostate cancer, BR. J. CANCER (2006)95:1186-1194). A portion of this cohort (but not including any of themen this experiment) was previously used for evaluating the clinicalutility of the CCP score as discussed in the Examples above. Patientsunique to this experiment, and not part of any previous evaluation ofCCP score or KLK3) are referred to herein as TURP1B. Patients wereexcluded from the present analysis if their clinical records weremissing information about PSA levels, Gleason score, or extent ofdisease. Clinical and molecular data were obtained for 303 individualswith 66 prostate cancer specific deaths for analyses with the CCP score,and 291 individuals for with 61 prostate cancer specific deaths for ouranalyses with KLK3. Patient data was censored at 10 years.

Statistics

Association between expression levels and prostate cancer-specificmortality were tested using univariate and multivariate Cox proportionalhazard models. Multivariate analysis was performed using relevantclinical parameters indicated below. Hazard ratios are reported per unitincrease in gene expression score (equivalent to a doubling in geneexpression).

Results

The CCP score significantly predicted prostate cancer-specific mortalityin the TURP1B samples. The univariate and multivariate summarystatistics are below:

Univariate: CCP p-value<10⁻¹⁵; HR=3.3 (2.5, 4.3)

Multivariate:

-   -   CCP p-value<10⁻⁵; HR=2.1 (1.5, 2.8)    -   Gleason p-value=0.00035    -   log PSA p-value=0.013

The prognostic utility of adding KLK3 to CCP score was also validated.In these analyses we used the negative of KLK3 expression, so thathigher values would correspond to increased risk, as they do for CCP.This is because, for KLK3, lower expression predicts higher risk ofrecurrence or prostate cancer-specific mortality. The univariate andmultivariate summary statistics are below:

Univariate: KLK3 p-value<10⁻⁶; HR=1.8 (95% CI 1.5, 2.2)

Multivariate:

-   -   CCP p-value<10⁻⁵; HR=2.2 (95% CI 1.6, 3.0)    -   KLK3 p-value 0.00019; HR=1.6 (93% CI 1.3, 2.1)    -   Gleason p-value=0.0055    -   log PSA p-value=0.055

Additional summary statistics for a bivariate analysis and amultivariate analysis are below:

Bivariate:

-   -   CCP p-value<10⁻¹³; HR=3.3 (95% CI 2.5, 4.4)    -   KLK3 p-value<10⁻⁴; HR=0.59 (95% CI 0.48, 0.71)

Multivariate (Multivariate Cox model adjusted for Gleason and PSA):

-   -   CCP p-value<10-5; HR=2.2 (95% CI 1.6, 3.0)    -   KLK3 p-value<10⁻³; HR=0.62 (0.48, 0.77)

In addition to KLK3, several other candidate genes were assessed fortheir ability to add independent prognostic information to the CCPscore. The results a summarized in FIG. 25, which shows univariatep-values for association with prostate cancer specific mortality(x-axis) and p-values after adjusting for CCP score (y-axis). Theadditional genes are listed in Table Y below (a subset of which formPanel I of the disclosure), ranked according to p-value after adjustingfor CCP score.

TABLE Y Gene Independent Adjusted for CCP score Example ABI Gene #Symbol pvalue hr hr.lcl hr.ucl pvalue hr hr.lcl hr.ucl Assay ID 1SLC45A3{circumflex over ( )} 3.01E−06 1.72 1.39 2.13 6.47E−07 1.82 1.452.28 Hs00263832_m1 2 ACPP{circumflex over ( )} 1.14E−09 1.71 1.46 1.993.09E−06 1.59 1.32 1.91 Hs00173475_m1 3 TRPM8{circumflex over ( )}5.54E−08 1.47 1.29 1.67 4.02E−06 1.39 1.22 1.59 Hs00375481_m1 4MSMB{circumflex over ( )} 1.65E−07 1.41 1.25 1.61 1.28E−05 1.33 1.171.51 Hs00159303_m1 5 KLK3{circumflex over ( )} 8.48E−07 1.77 1.44 2.172.21E−05 1.67 1.34 2.08 Hs03063374_m1 6 GTPBP5 9.79E−01 1.00 0.75 1.345.42E−05 2.04 1.44 2.88 Hs00534998_m1 7 IRF1 1.04E−02 1.50 1.10 2.041.43E−04 1.64 1.28 2.10 Hs00971965_m1 8 FOXA1 5.03E−01 1.13 0.80 1.582.50E−04 2.12 1.44 3.11 Hs00270129_m1 9 SLC30A4 2.24E−03 1.56 1.19 2.042.91E−04 1.78 1.31 2.41 Hs00203308_m1 10 AZGP1 1.18E−07 1.45 1.28 1.632.97E−04 1.32 1.15 1.52 Hs00426651_m1 11 MARC1 4.20E−01 1.15 0.82 1.603.10E−04 1.82 1.32 2.50 Hs00224227_m1 12 PTPRC 2.25E−02 1.35 1.04 1.743.51E−04 1.57 1.23 2.00 Hs00894732_m1 13 PCA3 2.53E−03 1.12 1.05 1.203.68E−04 1.14 1.07 1.22 Hs01371939_g1 14 PMEPA1 5.43E−04 1.84 1.30 2.614.38E−04 1.77 1.29 2.43 Hs00375306_m1 15 TMPRSS2 3.41E−04 1.39 1.20 1.616.13E−04 1.37 1.18 1.59 Hs01120965_m1 16 CDH1 5.57E−01 1.10 0.80 1.511.13E−03 1.67 1.25 2.24 Hs01023894_m1 17 NKX3 4.24E−02 1.46 1.03 2.081.75E−03 1.89 1.29 2.77 Hs00171834_m1 18 KLK2 1.57E−04 1.68 1.31 2.153.07E−03 1.58 1.19 2.10 Hs00428383_m1 19 SORD 8.49E−05 1.79 1.36 2.374.73E−03 1.51 1.14 2.01 Hs00973148_m1 20 IRF4 2.07E−01 1.14 0.93 1.418.35E−03 1.33 1.07 1.65 Hs00180031_m1 21 TARP; 1.18E−03 1.50 1.19 1.881.66E−02 1.32 1.06 1.65 Hs00827007_m1 TRGC2 22 STX4 2.61E−01 1.40 0.782.54 1.93E−02 2.09 1.14 3.84 Hs00190266_m1 23 KLK4 8.50E−06 1.70 1.362.13 5.23E−02 1.30 1.00 1.69 Hs00191772_m1 24 KLK3 (alt. 3.56E−03 1.431.13 1.81 7.27E−02 1.28 0.98 1.66 Hs02576345_m1 assay) 25 HLA-DRA2.13E−02 1.42 1.06 1.89 1.11E−01 1.24 0.96 1.61 Hs00219575_m1 26 SIRT32.32E−01 1.21 0.89 1.65 1.55E−01 1.27 0.92 1.77 Hs00202030_m1 27 EIF3D1.44E−02 1.55 1.11 2.17 1.94E−01 1.24 0.90 1.71 Hs00388727_m1 28 IGJ4.28E−01 1.05 0.92 1.20 2.69E−01 1.08 0.94 1.24 Hs00950678_g1 29 HLA-1.47E−01 1.40 0.89 2.22 3.18E−01 1.24 0.81 1.91 Hs01072899_m1 DPA1 30IGLL5; 1.58E−01 0.85 0.67 1.06 3.49E−01 1.15 0.86 1.53 Hs00382306_m1CKAP2 31 HOXB13 4.16E−01 0.86 0.60 1.24 5.42E−01 0.88 0.58 1.33Hs00197189_m1 32 STEAP2 5.33E−02 1.66 0.99 2.78 7.87E−01 1.08 0.60 1.96Hs00537786_m1 33 AR 5.77E−01 0.91 0.64 1.29 8.47E−01 1.04 0.73 1.47Hs00171172_m1 34 CREB3L4 4.80E−01 1.10 0.85 1.43 9.24E−01 1.01 0.77 1.34Hs00370116_m1 35 MKI67 2.97E−12 0.40 0.32 0.52 9.83E−01 0.99 0.60 1.65Hs01032443_m1 36 HLA-E 8.24E−02 1.34 0.96 1.87 9.85E−01 1.00 0.74 1.36Hs03045171_m1 {circumflex over ( )}These genes form Panel I of thedisclosure * “hr” = hazard ratio; “hr.lcl” = hazard ratio lower 95%confidence limit; “hr.ucl” = hazard ratio upper 95% confidence limit

FIG. 26 shows a plot of the CCP score versus the KLK3 expression(−deltaCT). The resulting correlation coefficient of the plot is −0.21with a p-value of 0.0003. FIG. 27 shows prostate cancer survivalpercentage against years after diagnosis by CCP score intervals for theTURP1B cohort. The Cox PH p-value was <10⁻⁴ for continuous CCP. FIG. 28shows prostate cancer survival percentage against years after diagnosisby KLK3 intervals for the TURP1B cohort. The Cox PH p-value was <10⁻⁶for continuous KLK3.

Example 10

The prognostic utility of CCP genes and androgen signaling genes wereevaluated using assay techniques as discussed above. The androgensignaling gene, PCA3, was evaluated for its prognostic utility inprostate cancer. The analysis used the TURP1B cohort from above, theTAGP1 cohort, and the Hamburg cohort. The TAPG1 (Transatlantic ProstateGroup cohort 1) cohort has been described previously (Cuzick et al., Br.J. Cancer. 2006 Nov. 6; 95(9):1186-94). The Hamburg cohort (n=316)comprised patients treated for prostate cancer by radial prostatectomyat Martiniklinik (Martini Clinic) of University Medical CenterHamburg-Eppendorf (Universitasklinikum Hamburg-Eppendorf—UKE) from 2005to 2006. The patient samples from the Hamburg cohort were prepared assimulated biopsies by removing a tissue cylinder (diameter=0.6 mm) fromthe region of the post-surgical FFPE block containing the largest tumorfoci. The Hamburg cohort excluded patients with neoadjuvant therapy orPSA>100 ng/ml. The outcome measure for the Hamburg cohort was BCR (48events).

Table Z below shows the prognostic utility of CCP genes and PCA3 in theTURP1B cohort using univariate and multivariate analysis. The TURP1Bcohort comprised n=296, 64 events, and 10 year DSM.

TABLE Z Univariate Multivariate Variable HR p-value HR p-value CCP 3.4(2.6, 4.5) 1.1 × 10⁻¹⁶ 2.3 (1.7, 3.3) 3.6 × 10⁻⁷ PCA3  0.89 (0.84, 0.96)0.00025  0.91 (0.84, 0.97)  0.0082 Gleason <7 Reference ReferenceReference Reference Gleason 7  2.2 (1.06, 4.7) 5.6 × 10⁻¹⁴  1.2 (0.54,2.7) 0.014 Gleason >7 9.9 (5.3, 19)  2.7 (1.3, 5.9) Log (1 + PSA) 1.9(1.5, 2.4) 1.3 × 10⁻⁸  1.4 (1.1, 1.8) 0.017

Table AA below shows the prognostic utility of CCP genes and PCA3 in theHamburg cohort using univariate and multivariate analysis. The Hamburgcohort comprised n=264, 40 events, and 5 year BCR.

TABLE AA Univariate Multivariate Variable HR p-value HR p-value CCP  2.2(1.6, 3.1) 1.3 × 10⁻⁵  2.1 (1.5, 3.0) 0.00011 PCA3 0.86 (0.79, 0.95)0.0048  0.81 (0.73, 0.89) 0.00014 Gleason Reference Reference ReferenceReference <7 Gleason 7  2.5 (1.2, 5) 0.00011  1.2 (0.58, 2.6) 0.058 Gleason  8.7 (3.5, 22)  3.5 (1.3, 9.2) >7 Log (1 +  3.0 (1.8, 5.0) 6.6 ×10⁻⁵  2.9 (1.8, 4.8) 9.2 × 10⁻⁵ PSA)

Table BB below shows the prognostic utility of CCP genes and PCA3 in theTAPG1 cohort using univariate and multivariate analysis. The TAPG1cohort comprised n=195, 49 events, and 10 year DSM.

TABLE BB Univariate Multivariate Variable HR p-value HR p-value CCP 2.12.0 × 10⁻⁶ 1.6 0.0027 (1.5, 2.8) (1.2, 2.2) PCA3 0.86 4.1 × 10⁻⁵ 0.900.0038 (0.80, 0.92) (0.84, 0.97) Gleason < 7 Reference ReferenceReference Reference Gleason 7 1.5 1.7 × 10⁻⁵ 1.04 0.26 (0.62, 3.9)(0.40, 2.7) Gleason > 7 5.4 1.8 (2.2, 13) (0.65, 5.2) Log (1 + PSA) 1.70.0054 1.5 0.46 (1.2, 2.4) (1.0, 2.2)

Table CC below shows the prognostic utility of CCP genes and PCA3 in thecombined analysis of TURP1B, Hamburg, and TAPG1 cohorts using univariateand multivariate analysis. The combined cohort comprised n=755, and 153events.

TABLE CC Univariate Multivariate Variable HR p-value HR p-value CCP 2.65.6 × 10⁻²⁴ 1.9  2.1 × 10⁻¹¹ (2.1, 3.0) (1.6, 2.3) PCA3 0.87 8.6 × 10⁻⁹ 0.90 3.2 × 10⁻⁶ (0.84, 0.91) (0.86, 0.94) Gleason < 7 ReferenceReference Reference Reference Gleason 7 2.2 6.9 × 10⁻²² 1.3 0.00042(1.4, 3.4) (0.84, 2.1) Gleason > 7 8.4 2.7 (5.4, 13) (1.6, 4.6) Log (1 +PSA) 1.9 5.3 × 10⁻¹³ 1.5 1.0 × 10⁻⁵ (1.6, 2.3) (1.3, 1.9)

Using the Hamburg cohort, other candidate genes were assessed for theirprognostic utility. The candidate genes were assessed for their abilityto add independent prognostic information to the CCP score. FIG. 29summarizes the analysis and plots the candidate genes by univariatep-values (x-axis) and p-values after adjusting for CCP score (y-axis).

Example 11

The prognostic utility of using a combined score threshold to identifyindividuals who would qualify for active surveillance was investigated.A threshold for Active Surveillance (AS) was predefined based onprostate biopsy commercial combined score results. We selected 385patients who had been diagnosed with prostate cancer after 2005, hadgood quality samples (housekeeper gene qPCR C_(t) mean of <22CT), andmet the following clinical criteria for AS:

-   -   Gleason<7    -   PSA<10 ng=ml    -   <25% positive cores    -   T-stage T1c or T2a (however, we included 33 T1a and 17 T1b        patients from our clinical population).

Combined scores were calculated for the commercial samples according toExample 8 (also referred to as CCR, or CCR score). We selected the 90thpercentile of combined (CCR) scores for clinically AS-eligible patients.A first threshold was CCR=0.8, with the criteria for AS that CCR≤0.8(see FIG. 30). A second threshold was selected as CCR=0.6.

The performance characteristics of the threshold were then evaluated intwo independent cohorts of conservatively managed men with prostatecancer (TAPG1 [N=180] and TAPG2 [N=585]). A threshold of CCR=0.6corresponded to a 2.4% risk of disease specific mortality (DSM) within10 years in the TAPG-1 needle biopsy cohort, and 2.8% in TAPG-2. Thethreshold of CCR=0.8, corresponded to a 2.8% risk of DSM within 10 yearsin the TAPG-1 needle biopsy cohort, and a 3.3% risk in TAPG-2 (see TableDD—% risk of DSM within 10 years of diagnosis). The number ofindividuals qualifying for AS for CCR≤0.8 is shown in Table EE (prostatecancer deaths for each grouping shown in parentheses).

TABLE DD % risk % risk % risk TAPG-1 AS-threshold TAPG-1 TAPG-2 andTAPG-2 CCR = 0.6 2.4 2.8 2.7 CCR = 0.8 2.8 3.3 3.2

TABLE EE TAPG-1 and TAPG-1 TAPG-2 TAPG-2 AS-qualification Total (deaths)Total (deaths) Total (deaths) AS = No 178 (33) 525 (87) 703 (120) CCR >0.8 AS = Yes  2 (0) 60 (0) 62 (0)  CCR ≤ 0.8

Both thresholds dichotomized the TAPG-2 cohort into high and low riskgroups with significantly different survival (FIGS. 31 and 32). Notethat 10-year censoring was applied for all risk calculations. There wereno prostate cancer deaths prior to 10 years in the AS-eligible group,defined by either threshold. The log-rank test p-value comparing thesurvival curves for the dichotomized groups was 0.016 for the CR=0.6threshold (32 AS-eligible patients, or 5.5% of the cohort); and 0.00080for the CR=0.8 threshold (60 AS-eligible patients, or 10.3% of thecohort).

We have also evaluated the CCR=0.8 threshold in a commercially-testedcohort (N=1718) (FIG. 3). Twenty-nine percent of patients in this cohortwould qualify for AS on clinical parameters alone. Fifty-five percent ofpatients tested fall below the AS threshold. Ninety percent ofindividuals who qualify for AS based on clinical parameters alone alsofall below the CCR threshold for AS. 41% of patients who do not qualifyfor AS based on clinical parameters alone fall below the CCR threshold.

Table 1 below provides a large, but not exhaustive, list of CCGs.

TABLE 1 Gene (Name and/or Symbol) or Number (EST, cDNA clone, orAccession) 1 STK15: serine/threonine kinase 15 Hs.48915 R11407 2 PLK:polo (Drosophia)-like kinase Hs.77597 AA629262 3 UBCH10: ubiquitincarrier protein E2-C Hs.93002 AA430504 4 MAPK13: mitogen-activatedprotein kinase 13 Hs.178695 AA157499 p38delta mRNA = stress-activatedprotein kinase 4 5 CDC2: cell division cycle 2, G1 to S and G2 to MHs.184572 AA598974 6 TOP2A: topoisomerase (DNA) II alpha (170 kD)Hs.156346 AA504348 7 CENPE: centromere protein E (312 kD) Hs.75573AA402431 CENP-E = putative kinetochore motor that accumulates just befo8 TOP2A: topoisomerase (DNA) II alpha (170 kD) Hs.156346 AA026682 9KPNA2: karyopherin alpha 2 (RAG cohort 1, importin alpha 1) Hs.159557AA676460 10 FLJ10468: hypothetical protein FLJ10468 Hs.48855 N63744 11CCNF: cyclin F Hs.1973 AA676797 12 DKFZp762E1312: hypothetical proteinDKFZp762E1312 Hs.104859 T66935 13 CKS2: CDC2-Associated Protein CKS2Hs.83758 AA292964 14 C20ORF1: chromosome 20 open reading frame 1 Hs.9329H73329 15 BUB1: budding uninhibited by benzimidazoles 1 (yeast homolog)Hs.98658 AA430092 BUB1 = putative mitotic checkpoint protein ser/thrkinase 16 TOP2A: **topoisomerase (DNA) II alpha (170 kD) Hs.156346AI734240 17 CKS2: CDC2-Associated Protein CKS1 Hs.83758 AA010065 ckshs2= homolog of Cks1 = p34Cdc28/Cdc2-associated protein 18 ARL6IP:ADP-ribosylation factor-like 6 interacting protein Hs.75249 H20558 19L2DTL: L2DTL protein Hs.126774 R06900 20 STK15: **serine/threoninekinase 15 Hs.48915 H63492 aurora/IPL1-related kinase 21 E2-EPF:ubiquitin carrier protein Hs.174070 AA464019 22 UBCH10: ubiquitincarrier protein E2-C Hs.93002 R80790 23 KNSL5: kinesin-like 5 (mitotickinesin-like protein 1) Hs.270845 AA452513 Mitotic kinesin-likeprotein-1 24 CENPF: centromere protein F (350/400 kD, mitosin) Hs.77204AA701455 25 CCNA2: cyclin A2 Hs.85137 AA608568 Cyclin A 26 CDC2: celldivision cycle 2, G1 to S and G2 to M Hs.184572 AA278152 CDC2 = Celldivision control protein 2 homolog = P34 protein kin 27 HMMR:**hyaluronan-mediated motility receptor (RHAMM) Hs.72550 AA171715 28KIAA0008: KIAA0008 gene product Hs.77695 AA262211 29 HSPC145: HSPC145protein Hs.18349 R22949 30 FLJ20510: hypothetical protein FLJ20510Hs.6844 N53214 31 Homo sapiens NUF2R mRNA, complete cds Hs.234545AA421171: 32 HSPC216: hypothetical protein Hs.13525 T87341 33 P37NB: 37kDa leucine-rich repeat (LRR) protein Hs.155545 AA423870 34 CDC20: 35CCNE1: cyclin E1 Hs.9700 T54121 36 ESTs: Hs.221754 R84407 37 FLJ11252:hypothetical protein FLJ11252 Hs.23495 N30185 38 LOC51203: clone HQ0310PRO0310p1 Hs.279905 AA620485 39 FLJ10491: hypothetical protein FLJ10491Hs.274283 AA425404 40 KNSL1: kinesin-like 1 Hs.8878 AA504625 41 CENPA:centromere protein A (17 kD) Hs.1594 AI369629 42 Homo sapiens, cloneIMAGE: 2823731, mRNA, partial cds Hs.70704 R96941: 43 CDC6: CDC6 (celldivision cycle 6, S. cerevisiae) homolog Hs.69563 H59203 44 Homo sapiensDNA helicase homolog (PIF1) mRNA, partial cds Hs.112160 AA464521: 45ESTs: Hs.48480 AA135809 46 TSN: translin Hs.75066 AA460927 47 KPNA2:karyopherin alpha 2 (RAG cohort 1, importin alpha 1) Hs.159557 AA48908748 RRM2: ribonucleotide reductase M2 polypeptide Hs.75319 AA187351 49ESTs: Hs.14119 AA204830 50 CCNB1: cyclin B1 Hs.23960 R25788 51 GTSE1:G-2 and S-phase expressed 1 Hs.122552 AI369284 52 C20ORF1: chromosome 20open reading frame 1 Hs.9329 AA936183 53 TACC3: transforming, acidiccoiled-coil containing protein 3 Hs.104019 AA279990 JkR1 mRNAdownregulated upon T-cell activation 54 E2F1: E2F transcription factor 1Hs.96055 H61303 55 BUB1B: budding uninhibited by benzimidazoles 1 (yeasthomolog), beta Hs.36708 AA488324 56 ESTs,: Weakly similar to CGHU7Lcollagen alpha 1(III) chain precursor [H. sapiens] Hs.19322 AA088457 57KIAA0074: KIAA0074 protein Hs.1192 N54344 58 MPHOSPH1: M-phasephosphoprotein 1 Hs.240 AA282935 59 ANLN: anillin (Drosophila Scrapshomolog), actin binding protein Hs.62180 R12261 60 BIRC5: baculoviralIAP repeat-containing 5 (survivin) Hs.1578 AA460685 Survivin = apoptosisinhibitor = effector cell protease EPR-1 61 PTTG1: pituitarytumor-transforming 1 Hs.252587 AA430032 62 KIAA0159: chromosomecondensation-related SMC-associated protein 1 Hs.5719 AA668256 63 ESTs,:Weakly similar to OS-4 protein [H. sapiens] Hs.18714 W93120 64 HMMR:hyaluronan-mediated motility receptor (RHAMM) Hs.72550 R10284 65DKFZp762E1312: hypothetical protein DKFZp762E1312 Hs.104859 AA936181 66CKAP2: cytoskeleton associated protein 2 Hs.24641 T52152 67 RAMP:RA-regulated nuclear matrix-associated protein 68 SMAP: thyroid hormonereceptor coactivating protein Hs.5464 AA481555 69 FLJ22624: hypotheticalprotein FLJ22624 Hs.166425 AA488791 70 CKS1: CDC2-Associated ProteinCKS1 Hs.77550 N48162 71 NEK2: NIMA (never in mitosis gene a)-relatedkinase 2 Hs.153704 W93379 72 MKI67: antigen identified by monoclonalantibody Ki-67 73 TTK: TTK protein kinase Hs.169840 AI337292 74 VEGFC:vascular endothelial growth factor C Hs.79141 H07899 vascularendothelial growth factor related protein VRP 75 CDKN3: cyclin-dependentkinase inhibitor 3 (CDK2-associated dual specificity phosphatase)Hs.84113 AA284072 CIP2 = Cdi1 = KAP1 phosphatase = G1/S cell cycle gene76 Homo sapiens NUF2R mRNA, complete cds Hs.234545 R92435: 77 Homosapiens cDNA FLJ10325 fis, clone NT2RM2000569 Hs.245342 AA235662: 78HSPC145: HSPC145 protein Hs.18349 AA628867 79 HSU54999: LGN proteinHs.278338 W92010 80 FLJ20333: hypothetical protein FLJ20333 Hs.79828R27552 81 KNSL2: kinesin-like 2 Hs.20830 N69491 82 ESTs: Hs.133294AI053446 83 **ESTs: Hs.41294 H95819 84 SMTN: smoothelin Hs.149098AA449234 85 FLJ23311: hypothetical protein FLJ23311 Hs.94292 N73916 86USF1: upstream transcription factor 1 Hs.247842 AA719022 87 LOC51203:clone HQ0310 PRO0310p1 Hs.279905 AA779949 88 ADH4: alcohol dehydrogenase4 (class II), pi polypeptide Hs.1219 AA007395 89 ESTs: Hs.186579AA960844 90 CCNB2: cyclin B2 Hs.194698 AA774665 91 Homo sapiens, Similarto gene rich cluster, C8 gene, clone MGC: 2577, mRNA, complete cdsHs.30114 AA634371: 92 ESTs: Hs.99480 AA485454 93 Homo sapiens IRE1b mRNAfor protein kinase/ribonuclease IRE1 beta, complete cds Hs.114905AA088442: 94 PCNA: proliferating cell nuclear antigen Hs.78996 AA450264PCNA = proliferating cell nuclear antigen 95 AA075920: 96 GTSE1: G-2 andS-phase expressed 1 Hs.122552 AA449474 97 CKS1: CDC2-Associated ProteinCKS1 Hs.77550 AA278629 98 CDC25B: cell division cycle 25B Hs.153752AA448659 cdc25B = M-phase inducer phosphatase 2 99 ESTs,: Weakly similarto unnamed protein product [H. sapiens] Hs.99807 AA489023 Unknown UGHs.99807 ESTs sc_id384 100 PCNA: proliferating cell nuclear antigenHs.78996 H05891 101 LTBP3: **latent transforming growth factor betabinding protein 3 Hs.289019 R60197 102 Homo sapiens mRNA; cDNADKFZp434D0818 (from clone DKFZp434D0818) Hs.5855 N95578: 103 ESTs:Hs.126714 AA919126 104 CIT: citron (rho-interacting, serine/threoninekinase 21) Hs.15767 H10788 105 LBR: lamin B receptor Hs.152931 AA099136106 E2F1: E2F transcription factor 1 Hs.96055 AA424949 107 AA699928: 108CDKN2C: cyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4)Hs.4854 N72115 p18-INK6 = Cyclin-dependent kinase 6 inhibitor 109 STK12:serine/threonine kinase 12 Hs.180655 H81023 ARK2 = aurora-related kinase2 110 ESTs: Hs.111471 AA682533 111 ESTs: Hs.44269 AA465090 112 MCM4:minichromosome maintenance deficient (S. cerevisiae) 4 Hs.154443AA485983 113 PMSCL1: **polymyositis/scleroderma autoantigen 1 (75 kD)Hs.91728 AA458994 Cyclin A 114 MKI67: antigen identified by monoclonalantibody Ki-67 Hs.80976 AA425973 Ki67 (long type) 115 ESTs: Hs.133294AI144063 116 CDC25B: cell division cycle 25B Hs.153752 H14343 cdc25B =M-phase inducer phosphatase 2 117 FOXM1: forkhead box M1 Hs.239 AA129552MPP2 = putative M phase phosphoprotein 2 118 FLJ11029: hypotheticalprotein FLJ11029 Hs.274448 AI124082 119 H2AFX: H2A histone family,member X Hs.147097 H95392 120 FLJ20333: hypothetical protein FLJ20333Hs.79828 AA147792 121 SLC17A2: solute carrier family 17 (sodiumphosphate), member 2 Hs.19710 H60423 122 Homo sapiens IRE1b mRNA forprotein kinase/ribonuclease IRE1 beta, complete cds Hs.114905 AA102368:123 ESTs: Hs.163921 AA573689 124 MCM5: minichromosome maintenancedeficient (S. cerevisiae) 5 (cell division cycle 46) Hs.77171 AA283961125 CDKN1B: cyclin-dependent kinase inhibitor 1B (p27, Kip1) Hs.238990AA630082 126 AA779865: 127 PTTG1: pituitary tumor-transforming 1Hs.252587 AI362866 128 RAD21: RAD21 (S. pombe) homolog Hs.81848 AA683102129 Homo sapiens cDNA FLJ10325 fis, clone NT2RM2000569 Hs.245342AA430511: 130 NEK2: NIMA (never in mitosis gene a)-related kinase 2Hs.153704 AA682321 131 FLJ20101: LIS1-interacting protein NUDE1, rathomolog Hs.263925 N79612 132 FZR1: Fzr1 protein Hs.268384 AA621026 133ESTs: Hs.120605 AI220472 134 KIAA0855: golgin-67 Hs.182982 AA098902 135SRD5A1: steroid-5-alpha-reductase, alpha polypeptide 1 (3-oxo-5alpha-steroid delta 4-dehydrogenase alpha 1) Hs.552 H16833 136 RAD51:RAD51 (S. cerevisiae) homolog (E coli RecA homolog) Hs.23044 N70010 137KNSL2: kinesin-like 2 Hs.20830 R11542 138 KIAA0097: KIAA0097 geneproduct Hs.76989 AA598942 139 TUBB: tubulin, beta polypeptide Hs.179661AA427899 140 HEC: highly expressed in cancer, rich in leucine heptadrepeats Hs.58169 W72679 141 TROAP: trophinin associated protein (tastin)Hs.171955 H94949 142 ESTs: Hs.49047 N64737 143 ESTs: Hs.15091 AA678348144 ESTs: Hs.133431 AI061169 145 KIAA0042: KIAA0042 gene product Hs.3104AA477501 146 FZR1: Fzr1 protein Hs.268384 AA862886 147 FEN1: flapstructure-specific endonuclease 1 Hs.4756 AA620553 148 CKS1:CDC2-Associated Protein CKS1 Hs.77550 AA459292 ckshs1 = homolog of Cks1= p34Cdc28/Cdc2-associated protein 149 ESTs: Hs.193379 N57936 150CASP8AP2: CASP8 associated protein 2 Hs.122843 H50582 151 BIRC2:baculoviral IAP repeat-containing 2 Hs.289107 R19628 c-IAP1 = MIHB = IAPhomolog B 152 CKAP2: cytoskeleton associated protein 2 Hs.24641 AA504130153 HLA-DRA: major histocompatibility complex, class II, DR alphaHs.76807 R47979 154 HBP: Hairpin binding protein, histone Hs.75257AA629558 155 FLJ10483: hypothetical protein FLJ10483 Hs.6877 H12254 156CASP3: caspase 3, apoptosis-related cysteine protease Hs.74552 R14760CASPASE- 3 = CPP32 isoform alpha = yama = cysteine protease 157 **ESTs,:Weakly similar to protein that is immuno-reactive with anti-PTHpolyclonal antibodies [H. sapiens] Hs.301486 AA088258 158 HMG2:high-mobility group (nonhistone chromosomal) protein 2 Hs.80684 AA019203159 PRO2000: PRO2000 protein Hs.46677 H58234 160 FLJ20333: hypotheticalprotein FLJ20333 Hs.79828 T48760 161 T56726: 162 TIMP1: tissue inhibitorof metalloproteinase 1 (erythroid potentiating activity, collagenaseinhibitor) Hs.5831 H80214 163 ESTs: Hs.102004 R94281 164 FLJ10858:hypothetical protein FLJ10858 Hs.134403 AA677552 165 Homo sapiens cDNAFLJ11883 fis, clone HEMBA1007178 Hs.157148 N62451: 166 RFC4: replicationfactor C (activator 1) 4 (37 kD) Hs.35120 N93924 replication factor C167 PRO2000: PRO2000 protein Hs.46677 N47113 168 ECT2: epithelial celltransforming sequence 2 oncogene Hs.132808 AI031571 169 ESTs: Hs.165909AA629538 170 PCF11: PCF11p homolog Hs.123654 AA053411 171 BIRC3:baculoviral IAP repeat-containing 3 Hs.127799 H48533 c-IAP2 = MIHC = IAPhomolog C = TNFR2-TRAF signalling complex prot 172 EST,: Weakly similarto dJ45P21.2 [H. sapiens] Hs.326451 AA931528 173 KIAA0952: KIAA0952protein Hs.7935 AA454989 174 KIF5B: kinesin family member 5B Hs.149436AA608707 175 DKFZP566C134: DKFZP566C134 protein Hs.20237 N39306 176ANLN: anillin (Drosophila Scraps homolog), actin binding proteinHs.62180 R17092 177 ORC1L: origin recognition complex, subunit 1 (yeasthomolog)-like Hs.17908 H51719 178 ESTs: Hs.14139 T77757 179 IFIT1:interferon-induced protein with tetratricopeptide repeats 1 Hs.20315AA074989 180 MGC5338: hypothetical protein MGC5338 Hs.99598 AA463627 181COPEB: core promoter element binding protein Hs.285313 AA013481 182UK114: translational inhibitor protein p14.5 Hs.18426 N72715 183 ESTs:Hs.265592 H67282 184 HMG4: high-mobility group (nonhistone chromosomal)protein 4 Hs.19114 AA670197 185 MDS025: hypothetical protein MDS025Hs.154938 AI225067 186 DKFZP564A122: DKFZP564A122 protein Hs.187991N53236 187 TSC22: transforming growth factor beta-stimulated proteinTSC-22 Hs.114360 AA664389 188 AAAS: aladin Hs.125262 AA916726 189 PLAG1:**pleiomorphic adenoma gene 1 Hs.14968 AA418251 190 FLJ23293:**hypothetical protein FLJ23293 similar to ARL-6 interacting protein-2Hs.31236 R91583 191 H11: protein kinase H11; small stress protein-likeprotein HSP22 Hs.111676 AA010110 192 POLD3: polymerase (DNA directed),delta 3 Hs.82502 AA504204 193 SERPINB3: serine (or cysteine) proteinaseinhibitor, clade B (ovalbumin), member 3 Hs.227948 AA292860 194 DNAJB1:DnaJ (Hsp40) homolog, subfamily B, member 1 Hs.82646 AA435948 195 ESTs:Hs.99480 AA458886 196 BUB3: BUB3 (budding uninhibited by benzimidazoles3, yeast) homolog Hs.40323 AA405690 197 TUBB2: tubulin, beta, 2Hs.251653 AI000256 198 Homo sapiens SNC73 protein (SNC73) mRNA, completecds Hs.293441 H28469: 199 BUB3: BUB3 (budding uninhibited bybenzimidazoles 3, yeast) homolog Hs.40323 H38804 200 FLJ20699:hypothetical protein FLJ20699 Hs.15125 AA459420 201 KIAA0013: KIAA0013gene product Hs.172652 N63575 202 ESTs: Hs.20575 N20305 203 CDC25C: celldivision cycle 25C Hs.656 W95000 cdc25C = M-phase inducer phosphatase 3204 FLJ11186: hypothetical protein FLJ11186 Hs.89278 AA394225 205 TOPK:PDZ-binding kinase; T-cell originated protein kinase Hs.104741 AA448898206 KIAA0165: extra spindle poles, S. cerevisiae, homolog of Hs.153479AA948058 207 LOC51659: HSPC037 protein Hs.108196 AA961752 208 ESTs:Hs.10338 AA436456 209 SUCLG2: succinate-CoA ligase, GDP-forming, betasubunit Hs.247309 AA465233 210 ZNF265: zinc finger protein 265 Hs.194718AA452256 211 SKP2: S-phase kinase-associated protein 2 (p45) Hs.23348R22188 212 NS1-BP: NS1-binding protein Hs.197298 AA486796 213 C21ORF50:chromosome 21 open reading frame 50 Hs.4055 AA416628 214 BIRC2:baculoviral IAP repeat-containing 2 Hs.289107 AA702174 215 BIRC3:baculoviral IAP repeat-containing 3 Hs.127799 AA002125 c- IAP2 = MIHC =IAP homolog C = TNFR2-TRAF signalling complex prot 216 INDO:indoleamine-pyrrole 2,3 dioxygenase Hs.840 AA478279 217 DEEPEST: mitoticspindle coiled-coil related protein Hs.16244 T97349 218 ESTs: Hs.105826AA534321 219 C20ORF1: chromosome 20 open reading frame 1 Hs.9329AI654707 220 Homo sapiens cDNA: FLJ21869 fis, clone HEP02442 Hs.28465R63929: 221 RGS3: regulator of G-protein signalling 3 Hs.82294 AI369623222 Homo sapiens DC29 mRNA, complete cds Hs.85573 AA186460: 223 MCM6:minichromosome maintenance deficient (mis5, S. pombe) 6 Hs.155462AA663995 224 NPAT: nuclear protein, ataxia-telangiectasia locus Hs.89385AA284172 NPAT = E14 = gene in ATM locus 225 KNSL6: kinesin-like 6(mitotic centromere-associated kinesin) Hs.69360 AA400450 226 HN1:hematological and neurological expressed 1 Hs.109706 AA459865 227 TUBA3:Tubulin, alpha, brain-specific Hs.272897 AA865469 228 ESTs: Hs.221197N55457 229 KIAA0175: KIAA0175 gene product Hs.184339 AA903137 230CLASPIN: homolog of Xenopus Claspin Hs.175613 AA857804 231 CTNNA1:**catenin (cadherin-associated protein), alpha 1 (102 kD) Hs.178452AA026631 232 ESTs: Hs.221962 AA229644 233 SMC4L1: SMC4 (structuralmaintenance of chromosomes 4, yeast)-like 1 Hs.50758 AA452095 234ICBP90: transcription factor Hs.108106 AA026356 235 EXO1: exonuclease 1Hs.47504 AA703000 236 Homo sapiens TRAF4 associated factor 1 mRNA,partial cds Hs.181466 T84975: 237 ESTs: Hs.186814 AA700879 238 FLJ11269:hypothetical protein FLJ11269 Hs.25245 R37817 239 SFPQ: splicing factorproline/glutamine rich (polypyrimidine tract-binding protein-associated) Hs.180610 AA425258 240 ZF: HCF-binding transcription factorZhangfei Hs.29417 AA164474 241 TUBA2: tubulin, alpha 2 Hs.98102 AA626698242 Homo sapiens mRNA; cDNA DKFZp434M0435 (from clone DKFZp434M0435)Hs.25700 N94435: 243 FLJ20530: **hypothetical protein FLJ20530 Hs.279521AA425442 244 BTEB1: basic transcription element binding protein 1Hs.150557 N80235 245 LOC51053: geminin Hs.234896 H51100 246 D21S2056E:DNA segment on chromosome 21 (unique) 2056 expressed sequence Hs.110757AI362799 247 HDAC3: histone deacetylase 3 Hs.279789 H88540 248 USP1:ubiquitin specific protease 1 Hs.35086 AA099033 249 C21ORF50: chromosome21 open reading frame 50 Hs.4055 AA135912 250 FLJ13046: **hypotheticalprotein FLJ13046 similar to exportin 4 Hs.117102 T95333 251 ESTs:Hs.181059 AA912032 252 FLJ22009: hypothetical protein FLJ22009 Hs.123253AA401234 253 ESTs: Hs.62711 AA056377 254 RAD51C: RAD51 (S. cerevisiae)homolog C Hs.11393 R37145 RAD51C = Recombination/repair Rad51-relatedprotein 255 ESTs: Hs.268919 H53508 256 Homo sapiens cDNA FLJ11381 fis,clone HEMBA1000501 Hs.127797 AA885096: 257 SAP30: sin3-associatedpolypeptide, 30 kD Hs.20985 AA126982 258 H4FG: H4 histone family, memberG Hs.46423 AA868008 259 TUBA1: tubulin, alpha 1 (testis specific)Hs.75318 AA180742 tubulin-alpha-4 260 DHFR: dihydrofolate reductaseHs.83765 R00884 DHFR = Dihydrofolate reductase 261 DHFR: dihydrofolatereductase Hs.83765 N52980 262 MGC5528: hypothetical protein MGC5528Hs.315167 AA934904 263 NNMT: nicotinamide N-methyltransferase Hs.76669T72089 264 TUBB: tubulin, beta polypeptide Hs.179661 AI672565 265HSPA1L: heat shock 70 kD protein-like 1 Hs.80288 H17513 HSP70-HOM = Heatshock 70 KD protein 1 266 TUBA1: **tubulin, alpha 1 (testis specific)Hs.75318 R36063 267 PRO1073: **PRO1073 protein Hs.6975 AA176999 CIP4 =Cdc42-interacting protein 4 268 POLD3: polymerase (DNA directed), delta3 Hs.82502 AI017254 269 ESTs,: Moderately similar to T50635 hypotheticalprotein DKFZp762L0311.1 [H. sapiens] Hs.47378 N38809 270 DKFZP564A122:DKFZP564A122 protein Hs.187991 N57723 271 LRRFIP1: **leucine rich repeat(in FLII) interacting protein 1 Hs.326159 T84633 272 ESTs: Hs.55468AA165312 273 ESTs: Hs.31444 H16772 274 AFAP: actin filament associatedprotein Hs.80306 R69355 275 CXCR4: chemokine (C—X—C motif), receptor 4(fusin) Hs.89414 T62491 CXC chemokine receptor 4 = fusin = neuropeptideY receptor = L3 276 MSH2: **mutS (E. coli) homolog 2 (colon cancer,nonpolyposis type 1) Hs.78934 AA679697 277 ESTs: Hs.48474 N62074 278AA677337: 279 ESTs,: Moderately similar to TBB2_HUMAN TUBULIN BETA-2CHAIN [H. sapiens] Hs.23189 AA629908 280 HP1-BP74: HP1-BP74 Hs.142442H79795 281 FLJ20101: LIS1-interacting protein NUDE1, rat homologHs.263925 AA459394 282 Homo sapiens mRNA; cDNA DKFZp434D1428 (from cloneDKFZp434D1428); complete cds Hs.321775 AA431268: 283 ESTs: Hs.265592AA992658 284 ESTs: 285 DDX11: DEAD/H (Asp-Glu-Ala-Asp/His) boxpolypeptide 11 (S. cerevisiae CHL1- like helicase) Hs.27424 AA402879 286CDC27: cell division cycle 27 Hs.172405 T81764 287 ARGBP2:Arg/Abl-interacting protein ArgBP2 Hs.278626 N89738 288 DKFZP564A122:DKFZP564A122 protein Hs.187991 AA025807 289 OPN3: opsin 3(encephalopsin) Hs.279926 AA150060 290 DKFZP566C134: DKFZP566C134protein Hs.20237 AA456319 291 KIAA0855: golgin-67 Hs.182982 H15101 292PIN: dynein, cytoplasmic, light polypeptide Hs.5120 AA644679 293 ESTs,:Weakly similar to LIP1_HUMAN PANCREATIC LIPASE RELATED PROTEIN 1PRECURSO [H. sapiens] Hs.68864 AA088857 294 HDAC3: histone deacetylase 3Hs.279789 AA973283 295 DONSON: downstream neighbor of SON Hs.17834AA417895 296 LOC51053: geminin Hs.234896 AA447662 297 FLJ10545:hypothetical protein FLJ10545 Hs.88663 AA460110 298 MAD2L1: MAD2(mitotic arrest deficient, yeast, homolog)-like 1 Hs.79078 AA481076mitotic feedback control protein Madp2 homolog 299 TASR2: TLS-associatedserine-arginine protein 2 Hs.3530 H11042 300 MCM6: minichromosomemaintenance deficient (mis5, S. pombe) 6 Hs.155462 N57722 301 CIT:citron (rho-interacting, serine/threonine kinase 21) Hs.15767 W69425 302**ESTs: Hs.205066 AA284803 303 ICAM1: intercellular adhesion molecule 1(CD54), human rhinovirus receptor Hs.168383 R77293 CD54 = ICAM-1 304KIAA0855: golgin-67 Hs.182982 AA456818 305 ESTs,: Weakly similar toputative p150 [H. sapiens] Hs.300070 R10422 306 DEEPEST: mitotic spindlecoiled-coil related protein Hs.16244 AI652290 307 MCM2: minichromosomemaintenance deficient (S. cerevisiae) 2 (mitotin) Hs.57101 AA454572 308Homo sapiens cDNA: FLJ22272 fis, clone HRC03192 Hs.50740 AA495943: 309WISP1: **WNT1 inducible signaling pathway protein 1 Hs.194680 T54850 310KIAA0855: golgin-67 Hs.182982 AA280248 311 TEM8: tumor endothelialmarker 8 Hs.8966 H58644 312 BITE: p10-binding protein Hs.42315 H96392313 RAN: RAN, member RAS oncogene family Hs.10842 AA456636 314 EZH2:enhancer of zeste (Drosophila) homolog 2 Hs.77256 AA428252 315 MCM4:minichromosome maintenance deficient (S. cerevisiae) 4 Hs.154443 W74071316 DKFZp434J0310: hypothetical protein Hs.278408 AA279657 Unknown UGHs.23595 ESTs sc_id6950 317 PPP1R10: protein phosphatase 1, regulatorysubunit 10 Hs.106019 AA071526 318 H11: protein kinase H11; small stressprotein-like protein HSP22 Hs.111676 H57493 319 ESTs,: Weakly similar toKIAA1074 protein [H. sapiens] Hs.200483 AA463220 320 ESTs,: Weaklysimilar to ALU8_HUMAN ALU SUBFAMILY SX SEQUENCE CONTAMINATION WARNINGENTRY [H. sapiens] Hs.226414 N72576 321 AA775033: 322 LOC51004: CGI-10protein Hs.12239 AA677920 323 ESTs: Hs.150028 AI292036 324 MCM6:minichromosome maintenance deficient (mis5, S. pombe) 6 Hs.155462AA976533 325 ESTs,: Moderately similar to T50635 hypothetical proteinDKFZp762L0311.1 [H. sapiens] Hs.47378 AA406348 326 UCP4: uncouplingprotein 4 Hs.40510 H60279 327 MSH5: mutS (E. coli) homolog 5 Hs.112193AA621155 328 ROCK1: Rho-associated, coiled-coil containing proteinkinase 1 Hs.17820 AA872143 329 KIAA0855: golgin-67 Hs.182982 AA694481330 AA705332: 331 CDC27: cell division cycle 27 Hs.172405 N47994 332DONSON: downstream neighbor of SON Hs.17834 AI732249 333 SH3GL2:SH3-domain GRB2-like 2 Hs.75149 R12817 334 PRC1: protein regulator ofcytokinesis 1 Hs.5101 AA449336 335 ESTs,: Weakly similar to unnamedprotein product [H. sapiens] Hs.99807 AA417744 Unknown UG Hs.119424 ESTssc_id2235 336 Human: clone 23719 mRNA sequence Hs.80305 AA425722 337Homo sapiens mRNA; cDNA DKFZp564O2364 (from clone DKFZp564O2364)Hs.28893 W90240: 338 ESTs,: Weakly similar to LIP1_HUMAN PANCREATICLIPASE RELATED PROTEIN 1 PRECURSO [H. sapiens] Hs.68864 AA132858 339TUBA3: Tubulin, alpha, brain-specific Hs.272897 AA864642 340 AI283530:341 ESTs: Hs.302878 R92512 342 PPP1R10: protein phosphatase 1,regulatory subunit 10 Hs.106019 T75485 343 SFRS5: splicing factor,arginine/serine-rich 5 Hs.166975 R73672 344 SFRS3: splicing factor,arginine/serine-rich 3 Hs.167460 AA598400 345 PRIM1: primase,polypeptide 1 (49 kD) Hs.82741 AA025937 DNA primase (subunit p48) 346FLJ20333: hypothetical protein FLJ20333 Hs.79828 H66982 347 HSPA8: heatshock 70 kD protein 8 Hs.180414 AA620511 348 C4A: complement component4A Hs.170250 AA664406 349 DKC1: dyskeratosis congenita 1, dyskerinHs.4747 AA052960 350 HP1-BP74: HP1-BP74 Hs.142442 T84669 351 ETV4: etsvariant gene 4 (E1A enhancer-binding protein, E1AF) Hs.77711 AA010400E1A-F = E1A enhancer binding protein = ETS translocation variant 352Homo sapiens cDNA: FLJ23037 fis, clone LNG02036, highly similar toHSU68019 Homo sapiens mad protein homolog (hMAD-3) mRNA Hs.288261 W42414Smad3 = hMAD-3 = Homologue of Mothers Against Decapentaplegic (M: 353KIAA0952: KIAA0952 protein Hs.7935 AA679150 354 STK9: serine/threoninekinase 9 Hs.50905 N80713 355 NXF1: **nuclear RNA export factor 1Hs.323502 R01238 356 FLJ12892: hypothetical protein FLJ12892 Hs.17731AA449357 357 UNG: uracil-DNA glycosylase Hs.78853 H15111 358 STK17B:**serine/threonine kinase 17b (apoptosis-inducing) Hs.120996 AA419485359 YWHAH: tyrosine 3-monooxygenase/tryptophan 5-monooxygenaseactivation protein, eta polypeptide Hs.75544 N69107 360 FLJ13154:hypothetical protein FLJ13154 Hs.25303 AA923560 361 LOC51116: CGI-91protein Hs.20776 AA459419 362 SSXT: synovial sarcoma, translocated to Xchromosome Hs.153221 N59206 363 KIAA0978: KIAA0978 protein Hs.3686AA485878 364 EST: Hs.147907 AI223432 365 FLJ23468: hypothetical proteinFLJ23468 Hs.38178 AA431741 366 FLJ10339: **hypothetical protein FLJ10339Hs.203963 N95450 367 BMP2: bone morphogenetic protein 2 Hs.73853AA011061 368 PIR51: RAD51-interacting protein Hs.24596 AI214426 369FLJ20364: hypothetical protein FLJ20364 Hs.32471 AA676296 370 EIF4A2:**eukaryotic translation initiation factor 4A, isoform 2 Hs.173912H54751 371 ESTs,: Weakly similar to MCAT_HUMAN MITOCHONDRIALCARNITINE/ACYLCARNITINE CARRIER PROTEIN [H. sapiens] Hs.27769 AA469975372 FLJ11323: hypothetical protein FLJ11323 Hs.25625 AA775600 373DKFZP564D0764: DKFZP564D0764 protein Hs.26799 AA460732 374 CTL2: CTL2gene Hs.105509 AA454710 375 ESTs: Hs.293419 AA775845 376 IFIT1:interferon-induced protein with tetratricopeptide repeats 1 Hs.20315AA489640 Interferon-induced 56-KDa protein 377 RBBP8:retinoblastoma-binding protein 8 Hs.29287 H23021 378 **Homo sapiensclone 25061 mRNA sequence Hs.183475 R38944: 379 Human: DNA sequence fromclone RP3-383J4 on chromosome 1q24.1-24.3 Contains part of a geneencoding a kelch motif containing protein, part of a novel gene encodinga protein similar to Aspartyl-TRNA sy Hs.117305 N29457 380 FLJ12888:hypothetical protein FLJ12888 Hs.284137 N68390 381 ESTs,: Weakly similarto IF38_HUMAN EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 8 [H.sapiens] Hs.222088 AI139629 382 ESTs: Hs.241101 AA133590 383 H4FI: H4histone family, member I Hs.143080 AI218900 384 SP38: zona pellucidabinding protein Hs.99875 AA400474 385 GABPB1: GA-binding proteintranscription factor, beta subunit 1 (53 kD) Hs.78915 H91651 386 LCHN:LCHN protein Hs.12461 AA029330 387 DKFZP564D0462: hypothetical proteinDKFZp564D0462 Hs.44197 N32904 388 LENG8: leukocyte receptor cluster(LRC) encoded novel gene 8 Hs.306121 AA464698 389 HIF1A:hypoxia-inducible factor 1, alpha subunit (basic helix-loop-helixtranscription factor) Hs.197540 AA598526 390 ESTs: Hs.93714 R09201 391FLJ23468: hypothetical protein FLJ23468 Hs.38178 AA454949 392DKFZP566C134: DKFZP566C134 protein Hs.20237 AA448164 393 PPP3CA: proteinphosphatase 3 (formerly 2B), catalytic subunit, alpha isoform(calcineurin A alpha) Hs.272458 W60310 394 HMGE: GrpE-like proteincochaperone Hs.151903 H55907 395 CDK7: cyclin-dependent kinase 7(homolog of Xenopus MO15 cdk-activating kinase) Hs.184298 R22624 CAK =cdk7 = NRTALRE = sdk = CDK activating kinase 396 ABCC5: **ATP-bindingcassette, sub-family C (CFTR/MRP), member 5 Hs.108660 AA186613 397AA477707: 398 **ESTs: Hs.15607 R92899 399 LOC57209: Kruppel-type zincfinger protein Hs.25275 N50827 400 FLJ20101: LIS1-interacting proteinNUDE1, rat homolog Hs.263925 R87716 401 KNSL4: kinesin-like 4 Hs.119324AA430503 402 E2F5: E2F transcription factor 5, p130-binding Hs.2331AA455521 E2F-5 = pRB- binding transcription factor 403 TMPO:thymopoietin Hs.11355 T63980 404 POLQ: polymerase (DNA directed), thetaHs.241517 AI057325 405 TGIF: TG-interacting factor (TALE familyhomeobox) Hs.90077 H51705 406 TRIP13: thyroid hormone receptorinteractor 13 Hs.6566 AA630784 407 GAS6: growth arrest-specific 6Hs.78501 AA461110 408 HN1: hematological and neurological expressed 1Hs.109706 AA035429 409 BARD1: BRCA1 associated RING domain 1 Hs.54089AA558464 410 DHFR: dihydrofolate reductase Hs.83765 AA424790 411AA490946: 412 ESTs: Hs.130435 AA167114 413 HSPA8: heat shock 70 kDprotein 8 Hs.180414 AA629567 414 RRM2: ribonucleotide reductase M2polypeptide Hs.75319 AA826373 415 FLJ20036: hypothetical proteinFLJ20036 Hs.32922 H59114 416 COPEB: core promoter element bindingprotein Hs.285313 AA055584 CPBP = CBA1 = DNA-binding protein 417FLJ10604: hypothetical protein FLJ10604 Hs.26516 N72697 418 ESTs,:Weakly similar to cDNA EST yk415c12.5 comes from this gene [C. elegans]Hs.108824 H97880 419 UBE2D3: **ubiquitin-conjugating enzyme E2D 3(homologous to yeast UBC4/5) Hs.118797 AA017199 420 FLJ10890:**hypothetical protein FLJ10890 Hs.17283 AA004210 421 ESTs: Hs.214410AA579336 422 OLR1: oxidised low density lipoprotein (lectin-like)receptor 1 Hs.77729 AA682386 423 FLJ13231: hypothetical protein FLJ13231Hs.156148 W92787 424 EST: Hs.323101 W40398 425 ESTs,: Weakly similar toR06F6.5b [C. elegans] Hs.180591 N59330 426 Homo sapiens cDNA: FLJ23285fis, clone HEP09071 Hs.90424 N26163: 427 Homo sapiens mRNA full lengthinsert cDNA clone EUROIMAGE 42408 Hs.284123 AA211446: 428 NFKB1: nuclearfactor of kappa light polypeptide gene enhancer in B-cells 1 (p105)Hs.83428 AA451716 NFkB1 = NF-kappaB p105 = p50 429 LOC58486:transposon-derived Buster1 transposase-like protein Hs.25726 AA630256430 Homo sapiens cDNA FLJ10976 fis, clone PLACE1001399 Hs.296323AA424756: 431 KIAA0182: KIAA0182 protein Hs.75909 AI023801 432 RANGAP1:Ran GTPase activating protein 1 Hs.183800 AA991855 433 PKMYT1:membrane-associated tyrosine- and threonine-specific cdc2-inhibitorykinase Hs.77783 AA478066 Myt1 kinase 434 HSPA8: heat shock 70 kD protein8 Hs.180414 H64096 435 LUC7A: cisplatin resistance-associatedoverexpressed protein Hs.3688 AA411969 436 RRM1: ribonucleotidereductase M1 polypeptide Hs.2934 AA633549 437 SET07: PR/SET domaincontaining protein 7 Hs.111988 AA421470 438 **ESTs,: Weakly similar toALU1_HUMAN ALU SUBFAMILY J SEQUENCE CONTAMINATION WARNING ENTRY [H.sapiens] Hs.193452 W96179 439 Homo sapiens clone 25058 mRNA sequenceHs.179397 R38894: 440 ESTs,: Weakly similar to KIAA0973 protein [H.sapiens] Hs.14014 AA780791 441 EST: Hs.105298 AA489813 442 CTCF:CCCTC-binding factor (zinc finger protein) Hs.57419 H89996 443 HRB:HIV-1 Rev binding protein Hs.171545 AA485958 444 **ESTs: Hs.294083AA447679 445 KIAA0878: KIAA0878 protein Hs.188006 AA599094 446 ESTs,:Weakly similar to ALUB_HUMAN !!!! ALU CLASS B WARNING ENTRY !!! [H.sapiens] Hs.180552 AA481283 447 OGT: O-linked N-acetylglucosamine(GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase)Hs.100293 AA425229 448 Homo sapiens mRNA for KIAA1700 protein, partialcds Hs.20281 N40952: 449 Human: DNA sequence from clone RP1-187J11 onchromosome 6q11.1-22.33. Contains the gene for a novel protein similarto S. pombe and S. cerevisiae predicted proteins, the gene for a novelprotein simila Hs.72325 AA159962 450 KIAA1265: KIAA1265 protein Hs.24936AA479302 451 H1F0: H1 histone family, member 0 Hs.226117 H57830 452ARGBP2: Arg/Abl-interacting protein ArgBP2 Hs.278626 H02525 453 ODF2:outer dense fibre of sperm tails 2 Hs.129055 AA149882 454 CD97: CD97antigen Hs.3107 AI651871 455 BMI1: **murine leukemia viral (bmi-1)oncogene homolog Hs.431 AA193573 456 POLG: polymerase (DNA directed),gamma Hs.80961 AA188629 457 XPR1: xenotropic and polytropic retrovirusreceptor Hs.227656 AA453474 458 ESTs: Hs.128096 AA971179 459 DNAJB1:DnaJ (Hsp40) homolog, subfamily B, member 1 Hs.82646 AA481022 460 ARL4:ADP-ribosylation factor-like 4 Hs.201672 AI142552 461 SFRS5: splicingfactor, arginine/serine-rich 5 Hs.166975 AA598965 462 ESTs: Hs.25933R11605 463 RIG-I: RNA helicase Hs.145612 AA126958 464 FLJ10339:hypothetical protein FLJ10339 Hs.203963 AA628231 465 DR1: down-regulatorof transcription 1, TBP-binding (negative cofactor 2) Hs.16697 AA043503466 Homo sapiens, Similar to hypothetical protein FLJ20093, clone MGC:1076, mRNA, complete cds Hs.298998 AA703249: 467 HSPC163: HSPC163protein Hs.108854 H98963 468 DKFZP564A122: DKFZP564A122 proteinHs.187991 R27345 469 FLJ10128: uveal autoantigen with coiled coildomains and ankyrin repeats Hs.49753 T47624 470 DSCR1: Down syndromecritical region gene 1 Hs.184222 AA629707 471 FLJ10342: hypotheticalprotein FLJ10342 Hs.101514 AA490935 472 Homo sapiens mRNA; cDNADKFZp586N1323 (from clone DKFZp586N1323) Hs.24064 R26176: 473 ESTs:Hs.4983 H59921 474 ESTs,: Weakly similar to ALUB_HUMAN !!!! ALU CLASS BWARNING ENTRY !!! [H. sapiens] Hs.117949 H91167 475 CDC45L: CDC45 (celldivision cycle 45, S. cerevisiae, homolog)-like Hs.114311 AA700904 476STAT5B: signal transducer and activator of transcription 5B Hs.244613AA280647 STAT5A/5B 477 Homo sapiens cDNA FLJ14028 fis, cloneHEMBA1003838 Hs.281434 AA454682: 478 KIAA1524: KIAA1524 proteinHs.151343 AI248987 479 CTSD: cathepsin D (lysosomal aspartyl protease)Hs.79572 AA485373 480 Homo sapiens, Similar to hypothetical proteinFLJ20093, clone MGC: 1076, mRNA, complete cds Hs.298998 AA682274: 481GTPBP2: GTP binding protein 2 Hs.13011 T67069 482 LOC51003: CGI-125protein Hs.27289 AA485945 483 VCL: vinculin Hs.75350 AA486727 484 KIF5B:kinesin family member 5B Hs.149436 AA046613 485 CDC25A: cell divisioncycle 25A Hs.1634 AA071514 486 LOC51141: insulin induced protein 2Hs.7089 AA045308 487 **ESTs,: Moderately similar to CALD_HUMAN CALDESMON[H. sapiens] Hs.117774 H48508 488 TBX3-iso: TBX3-iso protein Hs.267182T48941 489 KIAA0176: KIAA0176 protein Hs.4935 R44371 490 PRKAR1A:protein kinase, cAMP-dependent, regulatory, type I, alpha (tissuespecific extinguisher 1) Hs.183037 N25969 PKA-R1 alpha = cAMP-dependentprotein kinase type I-alpha-cata 491 ESTs: Hs.268991 H77818 492 ESTs,:Weakly similar to A53028 isopentenyl-diphosphate Delta-isomerase [H.sapiens] Hs.9270 R17362 493 ESTs,: Weakly similar to B34087 hypotheticalprotein [H. sapiens] Hs.120946 H50656 494 TRN2: karyopherin beta 2b,transportin Hs.278378 R08897 495 LMNA: lamin A/C Hs.77886 AA489582 496NFE2L2: nuclear factor (erythroid-derived 2)-like 2 Hs.155396 AA629687497 DKFZp762L0311: hypothetical protein DKFZp762L0311 Hs.16520 AA486418498 ESTs,: Weakly similar to S71752 giant protein p619 [H. sapiens]Hs.14870 T96829 499 Homo sapiens mRNA; cDNA DKFZp434A1315 (from cloneDKFZp434A1315); complete cds Hs.298312 AA991355: 500 E2IG4: hypotheticalprotein, estradiol-induced Hs.8361 R13844 501 RANGAP1: Ran GTPaseactivating protein 1 Hs.183800 AA485734 502 H1F0: H1 histone family,member 0 Hs.226117 W69399 503 KIAA0239: KIAA0239 protein Hs.9729AA454740 504 ESTs,: Weakly similar to ALU7_HUMAN ALU SUBFAMILY SQSEQUENCE CONTAMINATION WARNING ENTRY [H. sapiens] Hs.68647 R96804 505PRO0650: PRO0650 protein Hs.177258 N54333 506 DNAJB9: DnaJ (Hsp40)homolog, subfamily B, member 9 Hs.6790 AA045792 507 Homo sapiens cDNA:FLJ21971 fis, clone HEP05790 Hs.71331 AA774678: 508 LOC56996:**cation-chloride cotransporter-interacting protein Hs.119178 AA037466509 AP3D1: adaptor-related protein complex 3, delta 1 subunit Hs.75056AA630776 510 SGK: serum/glucocorticoid regulated kinase Hs.159640AA486082 sgk = putative serine/threonine protein kinase transcriptional511 HSPC148: hypothetical protein Hs.42743 R23666 512 MRPL19:mitochondrial ribosomal protein L19 Hs.75574 AA521243 KIAA0104 513AA455102: 514 ESTs: Hs.150325 AI278813 515 **ESTs: Hs.40527 AA029844 516HSPC145: HSPC145 protein Hs.18349 AI271431 517 KIAA0170: KIAA0170 geneproduct Hs.277585 H68789 518 FLJ11127: hypothetical protein Hs.91165T98200 519 KIAA0182: KIAA0182 protein Hs.75909 H05099 520 FLJ23151:hypothetical protein FLJ23151 Hs.137260 AA284259 521 AMD1:S-adenosylmethionine decarboxylase 1 Hs.262476 AA425692 522 FLJ10342:**hypothetical protein FLJ10342 Hs.101514 AA934516 523 SPS:SELENOPHOSPHATE SYNTHETASE; Human selenium donor protein Hs.124027AA486372 524 KIAA1586: KIAA1586 protein Hs.180663 AA779733 525 ICBP90:transcription factor Hs.108106 AA908902 526 Homo sapiens cDNA: FLJ21971fis, clone HEP05790 Hs.71331 AI002036: 527 ABCC2: ATP-binding cassette,sub-family C (CFTR/MRP), member 2 Hs.193852 R91502 528 ARHGDIB: Rho GDPdissociation inhibitor (GDI) beta Hs.83656 AA487426 LyGDI = RhoGDP-dissociation inhibitor 2 = RHO GDI 2 529 RAD53: protein kinase Chk2Hs.146329 AI653182 530 R96880: 531 TNFAIP3: tumor necrosis factor,alpha-induced protein 3 Hs.211600 AA433807 532 ESTs: Hs.26979 H23469 533AOC2: amine oxidase, copper containing 2 (retina-specific) Hs.143102N50959 534 Homo sapiens mRNA; cDNA DKFZp586N1323 (from cloneDKFZp586N1323) Hs.24064 R30941: 535 AA452872: 536 ESTs: Hs.124169 R58970537 ACYP1: acylphosphatase 1, erythrocyte (common) type Hs.18573 W78754538 SIL: TAL1 (SCL) interrupting locus Hs.323032 AA704809 539 AA016234:540 Homo sapiens mRNA; cDNA DKFZp566P1124 (from clone DKFZp566P1124)Hs.321022 N50895: 541 KIAA1067: KIAA1067 protein Hs.325530 AA099138 542SMC4L1: SMC4 (structural maintenance of chromosomes 4, yeast)-like 1Hs.50758 AA283006 543 ESTs: Hs.29074 R70174 544 SNK: serum-induciblekinase Hs.3838 AA460152 545 FANCG: Fanconi anemia, complementation groupG Hs.8047 AA427484 546 Homo sapiens cDNA: FLJ21531 fis, clone COL06036Hs.102941 N95440: 547 Homo sapiens mRNA; cDNA DKFZp547B086 (from cloneDKFZp547B086) Hs.36606 N48700: 548 C1ORF2: chromosome 1 open readingframe 2 Hs.19554 H11464 cote1 = ORF in glucocerebrosidase locus 549HTF9C: Hpall tiny fragments locus 9C Hs.63609 H17888 550 ATF4:activating transcription factor 4 (tax-responsive enhancer element B67)Hs.181243 AA600217 551 ESTs: Hs.101014 AA194941 552 CDC25A: celldivision cycle 25A Hs.1634 AA913262 553 TOPK: PDZ-binding kinase; T-celloriginated protein kinase Hs.104741 AI002631 554 ASIP: agouti(mouse)-signaling protein Hs.37006 AI220203 555 DKFZP564F013:**hypothetical protein DKFZp564F013 Hs.128653 R14908 556 ZNF265: zincfinger protein 265 Hs.194718 N66014 557 SLC30A1: solute carrier family30 (zinc transporter), member 1 Hs.55610 AA195463 558 ESTs: Hs.28462R63922 559 ESTs: Hs.114055 R27431 560 IL6: interleukin 6 (interferon,beta 2) Hs.93913 N98591 IL-6 561 H3F3B: H3 histone, family 3B (H3.3B)Hs.180877 AA608514 562 ESTs: Hs.81263 W81524 563 Homo sapiens cDNA:FLJ23538 fis, clone LNG08010, highly similar to BETA2 Human MEN1 regionclone epsilon/beta mRNA Hs.240443 AA400234: 564 AMD1:S-adenosylmethionine decarboxylase 1 Hs.262476 R82299 565 MAP3K2:mitogen-activated protein kinase kinase kinase 2 Hs.28827 AA447971 566NET1: neuroepithelial cell transforming gene 1 Hs.25155 R24543 567CHAF1A: chromatin assembly factor 1, subunit A (p150) Hs.79018 AA704459568 MGC5585: hypothetical protein MGC5585 Hs.5152 H50655 569 KIAA1598:KIAA1598 protein Hs.23740 H17868 570 PNN: pinin, desmosome associatedprotein Hs.44499 W86139 571 ESTs: Hs.238797 N70848 572 ESTs,: Weaklysimilar to ALUB_HUMAN !!!! ALU CLASS B WARNING ENTRY !!! [H. sapiens]Hs.180552 AA600192 573 PDGFA: platelet-derived growth factor alphapolypeptide Hs.37040 AA701502 574 Homo sapiens clone FLC0675 PRO2870mRNA, complete cds Hs.306117 AA443127: 575 ESTs: Hs.143375 AA001841 576TUBB: tubulin, beta polypeptide Hs.179661 H37989 577 MSH2: mutS (E.coli) homolog 2 (colon cancer, nonpolyposis type 1) Hs.78934 AA219060MSH2 = DNA mismatch repair mutS homologue 578 TOPBP1: topoisomerase(DNA) II binding protein Hs.91417 R97785 579 KIAA0869: KIAA0869 proteinHs.21543 R43798 580 H4FH: H4 histone family, member H Hs.93758 AA702781581 FLJ23293: hypothetical protein FLJ23293 similar to ARL-6 interactingprotein-2 Hs.31236 AA629027 582 **Homo sapiens cDNA: FLJ23538 fis, cloneLNG08010, highly similar to BETA2 Human MEN1 region clone epsilon/betamRNA Hs.240443 AA053165: 583 KIAA0978: KIAA0978 protein Hs.3686 N64780584 KIAA1547: KIAA1547 protein Hs.31305 AA057737 585 DKFZP761C169:hypothetical protein DKFZp761C169 Hs.71252 AA608709 586 WS-3: novelRGD-containing protein Hs.39913 AA449975 587 FRZB: frizzled-relatedprotein Hs.153684 H87275 588 BRCA1: breast cancer 1, early onsetHs.194143 H90415 BRCA1 = Mutated in breast and ovarian cancer 589 ESTs:Hs.4983 H22936 590 HSPC150: HSPC150 protein similar toubiquitin-conjugating enzyme Hs.5199 AA460431 591 Homo sapiens mRNA forKIAA1712 protein, partial cds Hs.29798 H54592: 592 FLJ11186:hypothetical protein FLJ11186 Hs.89278 AA504111 Unknown UG Hs.89278 ESTs593 ESTs,: Weakly similar to unnamed protein product [H. sapiens]Hs.118338 R25481 594 APEXL2: apurinic/apyrimidinic endonuclease(APEXnuclease)-like 2 protein Hs.154149 AI674393 595 CDR2: cerebellardegeneration-related protein (62 kD) Hs.75124 AA074613 596 ESTs:Hs.69662 AA459724 597 PSCD2L: pleckstrin homology, Sec7 and coiled/coildomains 2-like Hs.8517 AA464957 598 CRK: v-crk avian sarcoma virus CT10oncogene homolog Hs.306088 H75530 599 CCNE2: cyclin E2 Hs.30464 AA520999Unknown UG Hs.30464 cyclin E2 600 LOC51240: hypothetical protein Hs.7870AA988037 601 FLJ11259: hypothetical protein FLJ11259 Hs.184465 AA485877602 PTP4A1: protein tyrosine phosphatase type IVA, member 1 Hs.227777AA482193 603 Homo sapiens cDNA: FLJ22355 fis, clone HRC06344 Hs.288283AA026375: 604 Human: clone 23719 mRNA sequence Hs.80305 H43437 605 Homosapiens clone FLC0675 PRO2870 mRNA, complete cds Hs.306117 AA485453: 606MSE55: serum constituent protein Hs.148101 H73234 607 CFLAR: CASP8 andFADD-like apoptosis regulator Hs.195175 AA453766 608 Homo sapiens cDNA:FLJ22844 fis, clone KAIA5181 Hs.296322 AA975103: 609 Human: DNA sequencefrom clone RP11-371L19 on chromosome 20 Contains two novel genes, thegene for a novel protein similar to 40S ribosomal protein S10 (RPS10),ESTs, STSs, GSSs and five CpG islands Hs.19002 R00846 610 ESTs: Hs.60054R26390 611 ESTs,: Weakly similar to ALU7_HUMAN ALU SUBFAMILY SQ SEQUENCECONTAMINATION WARNING ENTRY [H. sapiens] Hs.325158 AA032084 612FLJ10980: hypothetical protein FLJ10980 Hs.29716 N45467 613 IFIT1:**interferon-induced protein with tetratricopeptide repeats 1 Hs.20315AA157787 614 ESTs: Hs.21734 AA429809 615 DKFZP434C245: DKFZP434C245protein Hs.59461 AA705518 616 RNPS1: RNA-binding protein S1, serine-richdomain Hs.75104 AA496837 617 FLJ13639: hypothetical protein FLJ13639Hs.101821 AA131681 618 PCF11: PCF11p homolog Hs.123654 W73749 619EIF4G3: eukaryotic translation initiation factor 4 gamma, 3 Hs.25732N92469 620 Homo sapiens cDNA: FLJ21971 fis, clone HEP05790 Hs.71331AA130595: 621 STAT1: signal transducer and activator of transcription 1,91 kD Hs.21486 AA079495 622 BIRC3: baculoviral IAP repeat-containing 3Hs.127799 R07870 623 HP1-BP74: HP1-BP74 Hs.142442 N20589 624 HSPC228:hypothetical protein Hs.267288 AI734268 625 KIAA0675: KIAA0675 geneproduct Hs.165662 AA454867 626 AMD1: S-adenosylmethionine decarboxylase1 Hs.262476 AA504772 627 EST: Hs.149338 AI249089 628 PWP1: nuclearphosphoprotein similar to S. cerevisiae PWP1 Hs.172589 AA485992 629AI336973: 630 DUSP4: dual specificity phosphatase 4 Hs.2359 AA444049 631FLJ12788: hypothetical protein FLJ12788 Hs.20242 AA497041 632 HSPC150:HSPC150 protein similar to ubiquitin-conjugating enzyme Hs.5199 AA985450633 FLJ11729: hypothetical protein FLJ11729 Hs.286212 W15533 634 KLF4:Kruppel-like factor 4 (gut) Hs.7934 H45668 635 FLJ11058: hypotheticalprotein FLJ11058 Hs.180817 N63911 636 FLJ23468: hypothetical proteinFLJ23468 Hs.38178 AA460299 637 ESTs: Hs.115315 AI278336 638 EBI3:Epstein-Barr virus induced gene 3 Hs.185705 AA425028 EBI3 = cytokinereceptor 639 ESTs: Hs.293797 N63988 640 MGAT2: mannosyl(alpha-1,6-)-glycoprotein beta-1,2-N- acetylglucosaminyltransferaseHs.172195 AA485653 641 H2BFQ: H2B histone family, member Q Hs.2178AA456298 642 NMB: neuromedin B Hs.83321 AI650675 643 SSR3: signalsequence receptor, gamma (translocon-associated protein gamma) Hs.28707AA453486 644 HSPC196: hypothetical protein Hs.239938 R78498 645 EST:Hs.44522 N33610 646 BRF1: butyrate response factor 1 (EGF-responsefactor 1) Hs.85155 AA723035 647 MAN1A2: mannosidase, alpha, class 1A,member 2 Hs.239114 H97940 648 KIAA1201: KIAA1201 protein Hs.251278AA427719 649 NUCKS: similar to rat nuclear ubiquitous casein kinase 2Hs.118064 AA158345 650 MAGEF1: MAGEF1 protein Hs.306123 AA425302 651Human: Chromosome 16 BAC clone CIT987SK-A-362G6 Hs.6349 N75498 652R40377: 653 AP3M2: adaptor-related protein complex 3, mu 2 subunitHs.77770 R14443 654 ESTs,: Weakly similar to 1207289A reversetranscriptase related protein [H. sapiens] Hs.272135 AA705010 655 Homosapiens mRNA for FLJ00116 protein, partial cds Hs.72363 AA159893: 656EIF4E: eukaryotic translation initiation factor 4E Hs.79306 AA193254 657Homo sapiens mRNA for hypothetical protein (TR2/D15 gene) Hs.180545N47285: 658 ESTs: Hs.99542 AA461474 659 CTNND1: catenin(cadherin-associated protein), delta 1 Hs.166011 AA024656 660 ESTs:Hs.188554 R75884 661 ZNF217: zinc finger protein 217 Hs.155040 R81830662 FLJ12892: hypothetical protein FLJ12892 Hs.17731 AI243595 663 ETV5:ets variant gene 5 (ets-related molecule) Hs.43697 AA460265 664 EST:Hs.251574 T54821 665 RPS25: ribosomal protein S25 Hs.113029 T98662 666CNN2: calponin 2 Hs.169718 AA284568 667 ESTs,: Weakly similar toplakophilin 2b [H. sapiens] Hs.12705 AA485365 668 PAPPA:pregnancy-associated plasma protein A Hs.75874 AA609463 669 TFF3:trefoil factor 3 (intestinal) Hs.82961 N74131 670 AI204264: 671DJ328E19.C1.1: hypothetical protein Hs.218329 AA486041 672 ME3: malicenzyme 3, NADP(+)-dependent, mitochondrial Hs.2838 AA779401 673 ESTs,:Weakly similar to IEFS_HUMAN TRANSFORMATION-SENSITIVE PROTEIN IEF SSP3521 [H. sapiens] Hs.43213 AA490554 674 FLJ13181: hypothetical proteinFLJ13181 Hs.301526 AA057266 675 KIAA1547: KIAA1547 protein Hs.31305AA136692 676 ZNF281: zinc finger protein 281 Hs.59757 N47468 677 Homosapiens cDNA: FLJ23260 fis, clone COL05804, highly similar to HSU90911Human clone 23652 mRNA sequence Hs.13996 AA463961: 678 ESTs: Hs.25933AA411392 679 NCBP1: nuclear cap binding protein subunit 1, 80 kDHs.89563 AA278749 nuclear cap binding protein 680 H2BFL: H2B histonefamily, member L Hs.239884 H70774 681 DKFZP564A122: DKFZP564A122 proteinHs.187991 H66150 682 NASP: nuclear autoantigenic sperm protein(histone-binding) Hs.243886 AA644128 683 **ESTs,: Weakly similar toKIAA0822 protein [H. sapiens] Hs.98368 AA422008 684 MAP2K6:mitogen-activated protein kinase kinase 6 Hs.118825 H07920 685 ESTs:Hs.158357 AA865842 686 GADD45A: growth arrest and DNA-damage-inducible,alpha Hs.80409 AA147214 GADD45 alpha = growth arrest andDNA-damage-inducible protein 687 DHFR: dihydrofolate reductase Hs.83765AA488803 688 AA151930: 689 Homo sapiens mRNA; cDNA DKFZp434P116 (fromclone DKFZp434P116); complete cds Hs.103378 AA431133: 690 Homo sapiensmRNA; cDNA DKFZp564D156 (from clone DKFZp564D156) Hs.9927 T55704: 691ESTs: Hs.32204 R93719 692 PRPSAP1: phosphoribosyl pyrophosphatesynthetase-associated protein 1 Hs.77498 R20005 693 ZNF42: zinc fingerprotein 42 (myeloid-specific retinoic acid-responsive) Hs.169832AA987906 694 **ESTs: Hs.43712 N25936 695 RUNX1: runt-relatedtranscription factor 1 (acute myeloid leukemia 1; aml1 oncogene)Hs.129914 AA146826 696 Homo sapiens mRNA; cDNA DKFZp547C244 (from cloneDKFZp547C244) Hs.9460 T64452: 697 TYMS: thymidylate synthetase Hs.82962AA663310 698 MGC5528: hypothetical protein MGC5528 Hs.315167 AA843451699 ESTs: Hs.268685 R22952 700 SFPQ: splicing factor proline/glutaminerich (polypyrimidine tract-binding protein- associated) Hs.180610AA418910 701 ESTs: Hs.155105 AI221390 702 FLJ10624: hypothetical proteinFLJ10624 Hs.306000 AA489592 703 TRIP8: thyroid hormone receptorinteractor 8 Hs.6685 AA425205 704 DNAJB6: DnaJ (Hsp40) homolog,subfamily B, member 6 Hs.181195 AA496105 705 ESTs: Hs.18331 T98244 706RBM14: RNA binding motif protein 14 Hs.11170 AA421233 707 SCYA2: smallinducible cytokine A2 (monocyte chemotactic protein 1, homologous tomouse Sig-je) Hs.303649 AA425102 MCP-1 = MCAF = small inducible cytokineA2 = JE = chemokine 708 MGC4161: hypothetical protein MGC4161 Hs.177688AI224867 709 TUBB2: tubulin, beta, 2 Hs.251653 AA888148 710 FLJ20280:hypothetical protein FLJ20280 Hs.270134 N74086 711 TERA: TERA proteinHs.180780 AA465096 712 CPS1: **carbamoyl-phosphate synthetase 1,mitochondrial Hs.50966 N68399 713 KIAA0802: KIAA0802 protein Hs.27657W55875 714 FYN: FYN oncogene related to SRC, FGR, YES Hs.169370 N22980715 Homo sapiens PRO2751 mRNA, complete cds Hs.283978 H12784: 716 CLTH:Clathrin assembly lymphoid-myeloid leukemia gene Hs.7885 AA441930 717CHMP1.5: CHMP1.5 protein Hs.42733 W85875 718 SMARCB1: SWI/SNF related,matrix associated, actin dependent regulator of chromatin, subfamily b,member 1 Hs.159971 AA446018 719 AA487823: SRF = c-fos serum responseelement-binding transcription facto 720 **ESTs: Hs.130741 AA608725 721Homo sapiens cDNA FLJ10976 fis, clone PLACE1001399 Hs.296323 R36085: 722FLJ20036: hypothetical protein FLJ20036 Hs.32922 N91145 723 C11ORF5:chromosome 11 open reading frame 5 Hs.121025 AA776702 724 AF3P21: SH3protein Hs.102929 N94372 725 LOC54104: hypothetical protein Hs.12871H05934 726 DF: D component of complement (adipsin) Hs.155597 AA233549727 CEP4: Cdc42 effector protein 4; binder of Rho GTPases 4 Hs.3903AA449061 728 KIF5B: kinesin family member 5B Hs.149436 AA644218 729MGC5627: hypothetical protein MGC5627 Hs.237971 H02336 730 G3BP:Ras-GTPase-activating protein SH3-domain-binding protein Hs.220689AA449834 731 ESTs: Hs.293987 AA229758 732 ESTs: Hs.36828 AA194796 733Homo sapiens mRNA for FLJ00101 protein, partial cds Hs.221600 W92262:734 Homo sapiens cDNA: FLJ21288 fis, clone COL01927 Hs.6019 R07184: 735ESTs,: Weakly similar to 1207289A reverse transcriptase related protein[H. sapiens] Hs.250594 H86813 736 Homo sapiens cDNA FLJ11941 fis, cloneHEMBB1000649 Hs.124106 AI301573: 737 ESTs: Hs.24908 H77726 738 TOB2:transducer of ERBB2, 2 Hs.4994 AA486088 739 ESTs: Hs.143900 AI193212 740Homo sapiens clone FLC0675 PRO2870 mRNA, complete cds Hs.306117 H16589:741 ESTs,: Weakly similar to KIAA0638 protein [H. sapiens] Hs.296288T83657 742 FLJ20039: hypothetical protein FLJ20039 Hs.267448 AA448268743 RPA2: replication protein A2 (32 kD) Hs.79411 R13557 744 GAS1:growth arrest-specific 1 Hs.65029 AA025819 745 Human: DNA sequence fromclone 967N21 on chromosome 20p12.3-13. Contains the CHGB gene forchromogranin B (secretogranin 1, SCG1), a pseudogene similar to part ofKIAA0172, the gene for a novel protein Hs.88959 R56678 746 ESTs:Hs.21175 AI341642 747 LBC: lymphoid blast crisis oncogene Hs.301946AA135716 748 ESTs: Hs.194595 R06761 749 MGC4707: hypothetical proteinMGC4707 Hs.291003 R14653 750 ZNF183: zinc finger protein 183 (RINGfinger, C3HC4 type) Hs.64794 AA132766 751 RAD18: postreplication repairprotein hRAD18p Hs.21320 R59197 752 EIF4EBP2: **eukaryotic translationinitiation factor 4E binding protein 2 Hs.278712 H15159 753 **Homosapiens mRNA; cDNA DKFZp586M0723 (from clone DKFZp586M0723) Hs.27860AA446650: 754 ORC3L: origin recognition complex, subunit 3 (yeasthomolog)-like Hs.74420 H99257 755 CDK7: cyclin-dependent kinase 7(homolog of Xenopus MO15 cdk-activating kinase) Hs.184298 AI311067 756USP10: ubiquitin specific protease 10 Hs.78829 AA455233 757 KIAA0733:TAK1-binding protein 2; KIAA0733 protein Hs.109727 AA931658 758 R89286:759 ALDH4: aldehyde dehydrogenase 4 (glutamate gamma-semialdehydedehydrogenase; pyrroline-5-carboxylate dehydrogenase) Hs.77448 AA181378760 IDN3: IDN3 protein Hs.225767 N62911 761 ESTs: Hs.50180 H48143 762MIG2: mitogen inducible 2 Hs.75260 H29252 763 KIAA0856: KIAA0856 proteinHs.13264 R12847 764 EST: Hs.47763 N54162 765 Homo sapiens mRNA; cDNADKFZp547C244 (from clone DKFZp547C244) Hs.9460 AA447553: 766 KIAA0855:golgin-67 Hs.182982 AA775625 767 ESTs,: Weakly similar to JH0148nucleolin - rat [R. norvegicus] Hs.30120 R54659 768 FLJ22313:hypothetical protein FLJ22313 Hs.30211 H52061 769 ESTs: Hs.71818AI028074 770 KIAA0618: KIAA0618 gene product Hs.295112 AA455506 771ESTs: Hs.59413 W93056 772 ESTs: Hs.165607 AA992090 773 UBAP: ubiquitinassociated protein Hs.75425 AA446016 774 HAN11: WD-repeat proteinHs.176600 AA725641 775 USP16: ubiquitin specific protease 16 Hs.99819AA489619 776 ESTs: Hs.67776 AA464963 777 SM-20: similar to rat smoothmuscle protein SM-20 Hs.6523 H56028 778 CCNG2: cyclin G2 Hs.79069AA489647 779 Homo sapiens mRNA; cDNA DKFZp566P1124 (from cloneDKFZp566P1124) Hs.321022 N62953: 780 FLJ20094: hypothetical proteinFLJ20094 Hs.29700 N95490 781 LOC51174: delta-tubulin Hs.270847 W33133782 Homo sapiens mRNA; cDNA DKFZp434I1820 (from clone DKFZp434I1820);partial cds Hs.14235 N52394: 783 FANCA: Fanconi anemia, complementationgroup A Hs.284153 AA644129 784 P5-1: MHC class I region ORF Hs.1845T58146 785 DNA2L: DNA2 (DNA replication helicase, yeast, homolog)-likeHs.194665 AA974495 KIAA0083 786 LOC51578: **adrenal gland protein AD-004Hs.279586 AA150301 787 ESTs: Hs.326417 AA913304 788 CDKN2D:cyclin-dependent kinase inhibitor 2D (p19, inhibits CDK4) Hs.29656R77517 p19-INK4D = Cyclin-dependent kinase 4 inhibitor D 789 FABP1:fatty acid binding protein 1, liver Hs.5241 AA682392 790 TERA: TERAprotein Hs.180780 AA906997 791 ESTs: Hs.145383 AI253072 792 SLC7A5:solute carrier family 7 (cationic amino acid transporter, y+ system),member 5 Hs.184601 AA419176 793 AXL: AXL receptor tyrosine kinaseHs.83341 H15336 axl = ufo = tyrosine kinase receptor 794 LOC57190:selenoprotein N Hs.8518 AA284276 795 ESTs: Hs.99037 AA443948 796 STCH:stress 70 protein chaperone, microsome-associated, 60 kD Hs.288799H85311 797 ESTs: Hs.88523 AA278591 Unknown UG Hs.88523 ESTs 798 ESD:**esterase D/formylglutathione hydrolase Hs.82193 AA250931 799 ESTs:Hs.122444 R31021 800 ESTs: Hs.283127 AI291262 801 KIAA0480: **KIAA0480gene product Hs.92200 H91332 802 HP1-BP74: HP1-BP74 Hs.142442 AA598791803 **ESTs,: Moderately similar to ALU1_HUMAN ALU SUBFAMILY J SEQUENCECONTAMINATION WARNING ENTRY [H. sapiens] Hs.144662 AA987667 804 TTF2:transcription termination factor, RNA polymerase II Hs.142157 AI023603805 ESTs: Hs.13740 T70541 806 DJ37E16.5: hypothetical protein dJ37E16.5Hs.5790 AA400021 807 CDH24: cadherin-like 24 Hs.155912 AI732266 808DJ465N24.2.1: **hypothetical protein dJ465N24.2.1 Hs.8084 AA932375 809ESTs,: Weakly similar to S57447 HPBRII-7 protein [H. sapiens] Hs.16346AA410490 810 Homo sapiens cDNA: FLJ23285 fis, clone HEP09071 Hs.90424AI005038: 811 KRAS2: v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogenehomolog Hs.184050 N95249 812 FLJ20038: hypothetical protein FLJ20038Hs.72071 H96090 813 ESTs,: Weakly similar to ALU4_HUMAN ALU SUBFAMILYSB2 SEQUENCE CONTAMINATION WARNING ENTRY [H. sapiens] Hs.28848 AA486607814 H2AFN: H2A histone family, member N Hs.134999 AI095013 815 RERE:arginine-glutamic acid dipeptide (RE) repeats Hs.194369 AA490249 816USP1: ubiquitin specific protease 1 Hs.35086 T55607 817 TIP47: cargoselection protein (mannose 6 phosphate receptor binding protein)Hs.140452 AA416787 818 KIAA0135: KIAA0135 protein Hs.79337 AA427740KIAA0135 = related to pim-1 kinase 819 ESTs: Hs.214410 T95273 820PPP1R2: protein phosphatase 1, regulatory (inhibitor) subunit 2Hs.267819 N52605 821 Homo sapiens cDNA: FLJ21210 fis, clone COL00479Hs.325093 AA978323: 822 CSNK2A2: casein kinase 2, alpha primepolypeptide Hs.82201 AA054996 823 HSRTSBETA: rTS beta protein Hs.180433N66132 824 FLJ13110: hypothetical protein FLJ13110 Hs.7358 AA431233 825ESTs: Hs.238797 N30704 826 FYN: FYN oncogene related to SRC, FGR, YESHs.169370 N35086 827 RBM8A: RNA binding motif protein 8A Hs.65648AA448402 828 ESTs: Hs.21906 AA608546 829 ESTs: Hs.128081 AA971042 830PP591: hypothetical protein PP591 Hs.118666 AA626336 831 N63866: 832HM74: putative chemokine receptor; GTP-binding protein Hs.137555 R02739833 MID1: midline 1 (Opitz/BBB syndrome) Hs.27695 AA598640 834 KIAA1586:KIAA1586 protein Hs.180663 AA938639 835 Homo sapiens clone CDABP0014mRNA sequence Hs.92679 AA443139: 836 HSU79274: protein predicted byclone 23733 Hs.150555 AA451900 837 AOC3: amine oxidase, coppercontaining 3 (vascular adhesion protein 1) Hs.198241 AA036974 838AA548037: 839 FLJ10154: hypothetical protein FLJ10154 Hs.179972 AA457133840 THBS1: thrombospondin 1 Hs.87409 AA464532 841 DNAJB6: DnaJ (Hsp40)homolog, subfamily B, member 6 Hs.181195 AA431203 842 KIAA1547: KIAA1547protein Hs.31305 AI216623 843 GATA2: GATA-binding protein 2 Hs.760R32405 844 ESTs: Hs.176950 R82522 845 KIAA1018: KIAA1018 protein Hs.5400AA156859 846 B4GALT1: **UDP-Gal:betaGlcNAc beta1,4-galactosyltransferase, polypeptide 1 Hs.198248 AA043795 847 HMGCR:3-hydroxy-3-methylglutaryl-Coenzyme A reductase Hs.11899 AA779417 848ESTs,: Weakly similar to 1819485A CENP-E protein [H. sapiens] Hs.167652H94466 849 ESTs: Hs.294088 AA971073 850 KIAA1637: coactivatorindependent of AF-2 (CIA); KIAA1637 protein Hs.288140 AA918007 851HSPC196: hypothetical protein Hs.239938 H66023 852 DR1: down-regulatorof transcription 1, TBP-binding (negative cofactor 2) Hs.16697 AA132007853 CG1I: putative cyclin G1 interacting protein Hs.10028 AA486444 854IGSF4: immunoglobulin superfamily, member 4 Hs.70337 AA487505 855 ESTs:Hs.179309 AA664350 856 HSPC163: HSPC163 protein Hs.108854 AA053139 857FLJ12788: hypothetical protein FLJ12788 Hs.20242 AI061317 858 FEM1B:FEM-1 (C. elegans) homolog b Hs.6048 H82273 859 FXR1: fragile X mentalretardation, autosomal homolog 1 Hs.82712 N62761 860 NCOA3: nuclearreceptor coactivator 3 Hs.225977 AA156793 861 H2BFB: H2B histone family,member B Hs.180779 N33927 862 ESTs: Hs.23830 AA460601 863 CDK7:cyclin-dependent kinase 7 (homolog of Xenopus MO15 cdk-activatingkinase) Hs.184298 AA031961 CAK = cdk7 = NRTALRE = sdk = CDK activatingkinase 864 FLJ20259: hypothetical protein FLJ20259 Hs.9956 T55949 865Homo sapiens cDNA FLJ20678 fis, clone KAIA4163 Hs.143601 T95823: 866RPS19: ribosomal protein S19 Hs.298262 T72208 867 Homo sapiens mRNA;cDNA DKFZp434M0420 (from clone DKFZp434M0420) Hs.326048 AA443976: 868TP53: tumor protein p53 (Li-Fraumeni syndrome) Hs.1846 R39356 p53 869FBI1: HIV-1 inducer of short transcripts binding protein Hs.104640R06252 870 GOT1: glutamic-oxaloacetic transaminase 1, soluble (aspartateaminotransferase 1) Hs.597 H22855 871 FLJ21434: hypothetical proteinFLJ21434 Hs.298503 AA680129 872 DNMT2: DNA(cytosine-5-)-methyltransferase 2 Hs.97681 R95731 873 ESTs: Hs.55272W02785 874 H2BFQ: H2B histone family, member Q Hs.2178 AA010223 875NFIC: nuclear factor I/C (CCAAT-binding transcription factor) Hs.184771N20996 876 NPTX1: neuronal pentraxin I Hs.84154 H22445 877 TLOC1:translocation protein 1 Hs.8146 AA450205 878 MGC5302: endoplasmicreticulum resident protein 58; hypothetical protein MGC5302 Hs.44970N39195 879 ACTR2: ARP2 (actin-related protein 2, yeast) homolog Hs.42915AA032090 880 AI287555: 881 ABCA7: ATP-binding cassette, sub-family A(ABC1), member 7 Hs.134514 AI668632 882 COL7A1: collagen, type VII,alpha 1 (epidermolysis bullosa, dystrophic, dominant and recessive)Hs.1640 AA598507 883 RFC2: replication factor C (activator 1) 2 (40 kD)Hs.139226 AA663472 884 FLJ22583: hypothetical protein FLJ22583 Hs.287700AA135836 885 **ESTs,: Weakly similar to ORF2 [M. musculus] Hs.172208AI820570 886 ESTs: Hs.21667 R15709 887 RBBP4: retinoblastoma-bindingprotein 4 Hs.16003 AA705035 888 Homo sapiens mRNA; cDNA DKFZp434J1027(from clone DKFZp434J1027); partial cds Hs.22908 R20166: 889 ESTs:Hs.166539 AI080987 890 NKTR: natural killer-tumor recognition sequenceHs.241493 AA279666 NK-tumor recognition protein = cyclophilin-relatedprotein 891 MUC1: mucin 1, transmembrane Hs.89603 AA486365 892 AP4B1:adaptor-related protein complex 4, beta 1 subunit Hs.28298 AA481045 893ESTs: Hs.94943 AA452165 894 MITF: microphthalmia-associatedtranscription factor Hs.166017 N66177 895 ESTs: Hs.183299 AA286914Unknown UG Hs.183299 ESTs sc_id2032 896 BAG3: BCL2-associated athanogene3 Hs.15259 AI269958 897 INSR: insulin receptor Hs.89695 AA001106 898TRIP: TRAF interacting protein Hs.21254 AA186426 899 EST: Hs.307975R22182 900 **Homo sapiens cDNA: FLJ23037 fis, clone LNG02036, highlysimilar to HSU68019 Homo sapiens mad protein homolog (hMAD-3) mRNAHs.288261 W72201: 901 HLA-DNA: major histocompatibility complex, classII, DN alpha Hs.11135 AA702254 Major histocompatibility complex, classII, DN alpha 902 FLJ10392: **hypothetical protein FLJ10392 Hs.20887AI261305 903 MPHOSPH1: **M-phase phosphoprotein 1 Hs.240 N63752 904STAG1: stromal antigen 1 Hs.286148 R36160 905 USP1: ubiquitin specificprotease 1 Hs.35086 AA970066 906 ESTs,: Moderately similar to ALU4_HUMANALU SUBFAMILY SB2 SEQUENCE CONTAMINATION WARNING ENTRY [H. sapiens]Hs.181315 AA448251 907 PA26: p53 regulated PA26 nuclear protein Hs.14125AA447661 908 ESTs,: Weakly similar to zinc finger protein [H. sapiens]Hs.71243 N92478 909 SH3PX1: SH3 and PX domain-containing protein SH3PX1Hs.7905 R69163 910 **Homo sapiens cDNA: FLJ22554 fis, clone HSI01092Hs.93842 H58317: 911 RPS25: ribosomal protein S25 Hs.113029 AA779404 912ESTs,: Weakly similar to A49134 Ig kappa chain V-I region [H. sapiens]Hs.5890 N34799 fra-2 = fos-related antigen 2 913 TXNRD1: thioredoxinreductase 1 Hs.13046 AA453335 Thioredoxin reductase 914 **ESTs:Hs.184378 N77828 915 GCSH: glycine cleavage system protein H(aminomethyl carrier) Hs.77631 R71327 916 Homo sapiens cDNA FLJ11904fis, clone HEMBB1000048 Hs.285519 AA447098: 917 NCOA3: nuclear receptorcoactivator 3 Hs.225977 H51992 AIB1 = Amplified in Breast Cancer =TRAM-1 = RAC3 = ACTR = CAGH16 = nucl 918 FLJ20159: hypothetical proteinFLJ20159 Hs.288809 R33122 919 IL7R: interleukin 7 receptor Hs.237868AA487121 920 RAB23: RAB23, member RAS oncogene family Hs.94769 AA134569921 ESTs: Hs.132493 AA923168 922 ESTs: Hs.87507 AA236015 923 SHC1: SHC(Src homology 2 domain-containing) transforming protein 1 Hs.81972R52960 924 KIAA1321: KIAA1321 protein Hs.24336 W37999 925 GLI:glioma-associated oncogene homolog (zinc finger protein) Hs.2693AI373071 926 ESTs: Hs.183299 AA291137 Unknown UG Hs.183299 ESTssc_id2032 927 GPRK6: G protein-coupled receptor kinase 6 Hs.76297AA291284 928 ESTs: Hs.93704 AA702684 929 CAPS: calcyphosine Hs.26685AA858390 930 Homo sapiens cDNA FLJ10976 fis, clone PLACE1001399Hs.296323 R27711: 931 C6: complement component 6 Hs.1282 N59396 932UBE2D3: ubiquitin-conjugating enzyme E2D 3 (homologous to yeast UBC4/5)Hs.118797 AA465196 933 DDX8: DEAD/H (Asp-Glu-Ala-Asp/His) boxpolypeptide 8 (RNA helicase) Hs.171872 AA465387 RNA helicase (HRH1) 934DKFZP434B168: DKFZP434B168 protein Hs.48604 N62684 935 FLJ10512:hypothetical protein FLJ10512 Hs.93581 T39933 936 Homo sapiens mRNA;cDNA DKFZp564F093 (from clone DKFZp564F093) Hs.18724 W87709: 937 F8A:coagulation factor VIII-associated (intronic transcript) Hs.83363AA463924 938 HSU53209: transformer-2 alpha (htra-2 alpha) Hs.24937AA465172 939 UBQLN2: ubiquilin 2 Hs.4552 R43580 940 EIF2C2: eukaryotictranslation initiation factor 2C, 2 Hs.193053 N93082 941 Homo sapiensmRNA for FLJ00012 protein, partial cds Hs.21051 H17645: 942 KIAA0841:KIAA0841 protein Hs.7426 R20299 943 KCNAB2: potassium voltage-gatedchannel, shaker-related subfamily, beta member 2 Hs.298184 H14383 944KIAA1637: coactivator independent of AF-2 (CIA); KIAA1637 proteinHs.288140 AA521358 945 ESTs: Hs.27379 H17455 946 FLJ11323: hypotheticalprotein FLJ11323 Hs.25625 R49707 947 SSP29: acidic protein rich inleucines Hs.84264 AA489201 948 ESTs: Hs.69280 AA486011 949 ADAMTS1: adisintegrin-like and metalloprotease (reprolysin type) withthrombospondin type 1 motif, 1 Hs.8230 AA057170 950 ESTs: Hs.43466N23889 951 MLLT4: myeloid/lymphoid or mixed-lineage leukemia (trithorax(Drosophila) homolog); translocated to, 4 Hs.100469 AA010818 952 ESTs:Hs.271034 AA406581 953 LMNB1: lamin B1 Hs.89497 AA983462 954 Homosapiens cDNA FLJ13547 fis, clone PLACE1007053 Hs.7984 AA629264: 955PTMS: parathymosin Hs.171814 R10451 956 H2AFL: H2A histone family,member L Hs.28777 AI268551 957 FLJ21603: hypothetical protein FLJ21603Hs.129691 R72794 958 FLJ13287: hypothetical protein FLJ13287 Hs.53263AA621725 959 CXCR4: chemokine (C—X—C motif), receptor 4 (fusin) Hs.89414AA479357 960 INSM1: insulinoma-associated 1 Hs.89584 R38640 961 FREQ:frequenin (Drosophila) homolog Hs.301760 H16821 962 LOC58486:transposon-derived Buster1 transposase-like protein Hs.25726 AA868020963 SMARCD1: SWI/SNF related, matrix associated, actin dependentregulator of chromatin, subfamily d, member 1 Hs.79335 H91691 964 ESTs:Hs.242998 T96522 965 INADL: PDZ domain protein (Drosophila inaD-like)Hs.321197 AA005153 966 ESTs,: Weakly similar to putative p150 [H.sapiens] Hs.37751 AA436174 967 MGC5338: hypothetical protein MGC5338Hs.99598 H50550 968 W85890: 969 NUCKS: similar to rat nuclear ubiquitouscasein kinase 2 Hs.118064 AI053436 970 Homo sapiens clone 25110 mRNAsequence Hs.27262 H18031: 971 AI333214: 972 GAS41: glioma-amplifiedsequence-41 Hs.4029 T62072 973 LOC51170: retinal short-chaindehydrogenase/reductase retSDR2 Hs.12150 N79745 974 H2BFG: **H2B histonefamily, member G Hs.182137 R98472 975 ABCC1: **ATP-binding cassette,sub-family C (CFTR/MRP), member 1 Hs.89433 AA424804 976 EFNA1: ephrin-A1Hs.1624 AA857015 977 Homo sapiens mRNA; cDNA DKFZp434A1014 (from cloneDKFZp434A1014); partial cds Hs.278531 H00596: 978 PPP2CA: proteinphosphatase 2 (formerly 2A), catalytic subunit, alpha isoform Hs.91773AA599092 979 ESTs,: Weakly similar to unnamed protein product [H.sapiens] Hs.118338 W85843 980 Homo sapiens cDNA FLJ11643 fis, cloneHEMBA1004366 Hs.111496 AA598803: 981 ESTs,: Moderately similar toALUE_HUMAN !!!! ALU CLASS E WARNING ENTRY !!! [H. sapiens] Hs.125407AA878944 982 ESTs,: Moderately similar to ALU1_HUMAN ALU SUBFAMILY JSEQUENCE CONTAMINATION WARNING ENTRY [H. sapiens] Hs.144662 AI191290 983KIAA0916: KIAA0916 protein Hs.151411 R91388 984 CDC25A: cell divisioncycle 25A Hs.1634 R09062 985 PRIM2A: primase, polypeptide 2A (58 kD)Hs.74519 R61073 986 DSP: desmoplakin (DPI, DPII) Hs.74316 H90899 987KIAA0101: KIAA0101 gene product Hs.81892 W68219 988 ESTs,: Weaklysimilar to putative p150 [H. sapiens] Hs.268026 AA411454 989 ESTs:Hs.18140 T97707 990 H2AFL: H2A histone family, member L Hs.28777AA457566 991 Homo sapiens mRNA for KIAA1700 protein, partial cdsHs.20281 H00287: 992 STAG3: stromal antigen 3 Hs.20132 AA453028 993ZNF207: zinc finger protein 207 Hs.62112 N59119 994 BMP6: bonemorphogenetic protein 6 Hs.285671 AA424833 995 ESTs,: Moderately similarto sertolin [R. norvegicus] Hs.91192 H60690 996 LOC51064: **glutathioneS-transferase subunit 13 homolog Hs.279952 W88497 997 NUCKS: similar torat nuclear ubiquitous casein kinase 2 Hs.118064 AA927182 998 ESTs,:Weakly similar to T00370 hypothetical protein KIAA0659 [H. sapiens]Hs.131899 W93155 999 FLJ13057: hypothetical protein FLJ13057 similar togerm cell-less Hs.243122 R23254 1000 ESTs: Hs.144796 AI219737 1001FLJ10511: hypothetical protein FLJ10511 Hs.106768 R25877 1002DKFZP564A122: DKFZP564A122 protein Hs.187991 N31577 1003 ODF2: outerdense fibre of sperm tails 2 Hs.129055 AA400407 1004 AMY2A: amylase,alpha 2A; pancreatic Hs.278399 R64129 1005 **ESTs,: Weakly similar toplakophilin 2b [H. sapiens] Hs.12705 N91589 1006 CYP1B1: cytochromeP450, subfamily I (dioxin-inducible), polypeptide 1 (glaucoma 3, primaryinfantile) Hs.154654 AA029776 1007 CAPN7: calpain 7 Hs.7145 N46420 1008FLJ20069: hypothetical protein FLJ20069 Hs.273294 AA229966 1009FLJ10618: hypothetical protein FLJ10618 Hs.42484 AA478847 1010 KIAA1637:**coactivator independent of AF-2 (CIA); KIAA1637 protein Hs.288140AA452531 1011 FLJ20004: **hypothetical protein FLJ20004 Hs.17311AA487895 1012 FLJ12892: hypothetical protein FLJ12892 Hs.17731 AA6703631013 PLU-1: putative DNA/chromatin binding motif Hs.143323 AA464869 1014**ESTs: Hs.36828 AA418448 1015 KIAA0586: KIAA0586 gene product Hs.77724AA905278 1016 MTHFD2: methylene tetrahydrofolate dehydrogenase (NAD+dependent), methenyltetrahydrofolate cyclohydrolase Hs.154672 AA4809941017 BRF1: **butyrate response factor 1 (EGF-response factor 1) Hs.85155AA424743 1018 TFAP2A: transcription factor AP-2 alpha (activatingenhancer-binding protein 2 alpha) Hs.18387 R38044 1019 VIL2: villin 2(ezrin) Hs.155191 AA411440 1020 SDC1: syndecan 1 Hs.82109 AA074511 1021RNTRE: related to the N terminus of tre Hs.278526 AA281057 1022 HSPC207:hypothetical protein Hs.75798 H99997 1023 FLJ22376: hypothetical proteinFLJ22376 Hs.29341 AI199155 1024 RNF10: ring finger protein 10 Hs.5094H73586 1025 PNN: pinin, desmosome associated protein Hs.44499 AA7073211026 FLJ20516: hypothetical protein FLJ20516 Hs.70811 AA122393 1027RPL13A: ribosomal protein L13a Hs.119122 AI254200 1028 H2BFB: H2Bhistone family, member B Hs.180779 AA885642 1029 OGT: O-linkedN-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase)Hs.100293 R13317 1030 KIAA0155: KIAA0155 gene product Hs.173288 AA1336841031 ILF2: interleukin enhancer binding factor 2, 45 kD Hs.75117 H956381032 Homo sapiens mRNA; cDNA DKFZp586I1518 (from clone DKFZp586I1518)Hs.21739 AA287917: 1033 PKNOX1: PBX/knotted 1 homeobox 1 Hs.158225AI350546 1034 KMO: **kynurenine 3-monooxygenase (kynurenine3-hydroxylase) Hs.107318 AA044326 1035 VCAM1: vascular cell adhesionmolecule 1 Hs.109225 H16591 CD106 = VCAM-1 1036 N54811: 1037 KIAA0618:KIAA0618 gene product Hs.295112 H81940 1038 MAFG: v-mafmusculoaponeurotic fibrosarcoma (avian) oncogene family, protein GHs.252229 N21609 MafG = basic-leucine zipper transcription factor 1039MATN2: matrilin 2 Hs.19368 AA071473 1040 HOXB4: homeo box B4 Hs.126666AA918749 1041 FLJ10466: hypothetical protein FLJ10466 Hs.121073 AA4536071042 FLJ22557: hypothetical protein FLJ22557 Hs.106101 AA127879 1043EST: Hs.149260 AI247680 1044 KIAA0677: KIAA0677 gene product Hs.155983AA026751 1045 EST: Hs.104123 AA197344 1046 UCP4: uncoupling protein 4Hs.40510 H94680 1047 EST: Hs.144224 N93807 1048 GATA2: GATA-bindingprotein 2 Hs.760 H00625 GATA-binding protein 2 1049 ESTs: Hs.14743H61082 1050 EST: Hs.116174 AA626786 1051 ITGB3: integrin, beta 3(platelet glycoprotein IIIa, antigen CD61) Hs.87149 AA666269 1052FLJ23399: hypothetical protein FLJ23399 Hs.299883 R19895 1053 ESTs:Hs.21734 N72976 1054 FLJ20425: hypothetical protein FLJ20425 Hs.71040AA424566 1055 CUL4A: cullin 4A Hs.183874 AA598836 1056 PTP4A1: proteintyrosine phosphatase type IVA, member 1 Hs.227777 R61007 proteintyrosine phosphatase PTPCAAX1 (hPTPCAAX1) 1057 ESTs: Hs.7913 N35592 1058GRO1: GRO1 oncogene (melanoma growth stimulating activity, alpha) Hs.789W46900 1059 ESTs,: Moderately similar to NRD2 convertase [H. sapiens]Hs.309734 H78796 1060 FLJ10826: hypothetical protein FLJ10826 Hs.24809AA486738 1061 TOM34: translocase of outer mitochondrial membrane 34Hs.76927 AA457118 1062 H2AFL: H2A histone family, member L Hs.28777AA452933 1063 D10S170: **DNA segment, single copy, probe pH4(transforming sequence, thyroid- 1, Hs.315591 N35493 1064 SCYA2: smallinducible cytokine A2 (monocyte chemotactic protein 1, homologous tomouse Sig-je) Hs.303649 T77816 MCP-1 = MCAF = small inducible cytokineA2 = JE = chemokine 1065 FLJ10688: hypothetical protein FLJ10688Hs.118793 AA465358 1066 PTD017: PTD017 protein Hs.274417 AA160498 1067KIAA0026: MORF-related gene X Hs.173714 AA676604 1068 BMP2: bonemorphogenetic protein 2 Hs.73853 AA489383 1069 MNT: MAX binding proteinHs.25497 AA455508 1070 KIAA1170: KIAA1170 protein Hs.268044 H80507 1071CRYBA1: crystallin, beta A1 Hs.46275 AA487614 1072 KATNA1: katanin p60(ATPase-containing) subunit A 1 Hs.289099 AA609740 1073 Homo sapienscDNA FLJ20796 fis, clone COL00301 Hs.113994 N53458: 1074 CEP4: Cdc42effector protein 4; binder of Rho GTPases 4 Hs.3903 W32509 1075 ESTs:Hs.117261 AA682521 1076 CYP1B1: cytochrome P450, subfamily I(dioxin-inducible), polypeptide 1 (glaucoma 3, primary infantile)Hs.154654 AA040872 1077 ALTE: Ac-like transposable element Hs.9933AA630498 1078 RAD51: RAD51 (S. cerevisiae) homolog (E coli RecA homolog)Hs.23044 AA873056 1079 MAN1A2: mannosidase, alpha, class 1A, member 2Hs.239114 R78501 1080 H53763: 1081 MET: met proto-oncogene (hepatocytegrowth factor receptor) Hs.285754 AA410591 1082 DYRK1A: dual-specificitytyrosine-(Y)-phosphorylation regulated kinase 1A Hs.75842 AA676749 1083ARHGAP8: **Rho GTPase activating protein 8 Hs.102336 AA037410 1084 LMO4:LIM domain only 4 Hs.3844 H27986 1085 ADCY6: adenylate cyclase 6Hs.12373 AA148044 1086 EST: Hs.135448 AI078552 1087 NCOA3: nuclearreceptor coactivator 3 Hs.225977 W46433 1088 DNAJB4: DnaJ (Hsp40)homolog, subfamily B, member 4 Hs.41693 AA081471 1089 NAB1: NGFI-Abinding protein 1 (ERG1 binding protein 1) Hs.107474 AA486027 1090ESTs,: Weakly similar to T08663 hypothetical protein DKFZp547G0910.1 [H.sapiens] Hs.172084 N63646 1091 KIAA0735: KIAA0735 gene product; synapticvesicle protein 2B homolog Hs.8071 R56082 1092 GNB1: guanine nucleotidebinding protein (G protein), beta polypeptide 1 Hs.215595 AA487912 1093Homo sapiens mRNA for KIAA1716 protein, partial cds Hs.21446 R49763:1094 KINESIN: HEAVY CHAIN 1095 CCND1: cyclin D1 (PRAD1: parathyroidadenomatosis 1) Hs.82932 AA487486 Cyclin D1 = BCL1 = PRAD1 =Translocated in mantle cell leukemia 1096 ESTs: Hs.106129 R56716 1097AA431931: 1098 PSEN1: presenilin 1 (Alzheimer disease 3) Hs.3260AA403083 1099 ESTs: Hs.193804 AA010918 1100 DKFZp762P2111: hypotheticalprotein DKFZp762P2111 Hs.14217 AA429586 1101 KIAA1350: KIAA1350 proteinHs.101799 W37627 1102 FLJ20847: hypothetical protein FLJ20847 Hs.13479H16996 1103 HDCMA18P: HDCMA18P protein Hs.278635 N64387 1104 FLJ12890:hypothetical protein FLJ12890 Hs.43299 N62475 1105 ESTs: Hs.127453AA973625 1106 BAIAP2: BAI1-associated protein 2 Hs.7936 R60328 1107ESTs: Hs.317584 AA191424 1108 DKFZP434J046: DKFZP434J046 proteinHs.116244 AI024401 1109 ESTs: Hs.114055 AA701352 1110 ESTs: Hs.44380N93122 1111 ESTs: Hs.20142 AA625570 1112 UBL3: ubiquitin-like 3Hs.173091 T82438 1113 H2AFL: H2A histone family, member L Hs.28777N50797 1114 SUCLG2: **succinate-CoA ligase, GDP-forming, beta subunitHs.247309 N68557 1115 ZWINT: ZW10 interactor Hs.42650 AA706968 1116FLJ10583: hypothetical protein FLJ10583 Hs.105633 R00425 1117 FLJ20552:hypothetical protein FLJ20552 Hs.69554 AA463982 1118 FADD: Fas(TNFRSF6)-associated via death domain Hs.86131 AA430751 FADD = MORT 1119SFRS7: splicing factor, arginine/serine-rich 7 (35 kD) Hs.184167AA418813 1120 RAD54L: RAD54 (S. cerevisiae)-like Hs.66718 AI372035 1121MYLE: MYLE protein Hs.11902 T68845 1122 LOC51334: mesenchymal stem cellprotein DSC54 Hs.157461 R63841 1123 PRIM2A: primase, polypeptide 2A (58kD) Hs.74519 AA434404 1124 KIAA0056: KIAA0056 protein Hs.13421 AA4305451125 ESTs,: Moderately similar to ALU7_HUMAN ALU SUBFAMILY SQ SEQUENCECONTAMINATION WARNING ENTRY [H. sapiens] Hs.82590 N53024 1126 ESTs:Hs.117269 AA705050 1127 NSAP1: NS1-associated protein 1 Hs.155489AA186327 1128 CEACAM5: carcinoembryonic antigen-related cell adhesionmolecule 5 Hs.220529 AA130547 1129 FLJ11021: hypothetical proteinFLJ11021 similar to splicing factor, arginine/serine- rich 4 Hs.81648AA291183 Unknown UG Hs.202583 ESTs, Weakly similar to arginine-rich 1130FOSL1: FOS-like antigen-1 Hs.283565 T82817 fra-1 = fos-related antigen 11131 U3-55K: U3 snoRNP-associated 55-kDa protein Hs.153768 AA465355 1132DNAJC6: DnaJ (Hsp40) homolog, subfamily B, member 6 Hs.44896 AA4559401133 KIAA1382: amino acid transporter 2 Hs.298275 R27255 Similar totransporter protein 1134 PCAF: p300/CBP-associated factor Hs.199061N74637 P/CAF = p300/CBP-associated factor 1135 ESTs: Hs.130460 AA9272521136 ESTs: Hs.112570 AI014667 1137 FLJ10209: hypothetical proteinFLJ10209 Hs.260150 AA454626 1138 ESTs: Hs.99014 AA485679 1139 ESTs:Hs.99621 AA464707 1140 Homo sapiens cDNA FLJ11904 fis, cloneHEMBB1000048 Hs.285519 N74617: 1141 AA928536: 1142 SQSTM1:**sequestosome 1 Hs.182248 AA931964 1143 **Homo sapiens cDNA FLJ13700fis, clone PLACE2000216, highly similar to SPECTRIN BETA CHAIN, BRAINHs.324648 AA018591: 1144 SLC22A3: solute carrier family 22(extraneuronal monoamine transporter), member 3 Hs.81086 AA460012 1145FLJ22557: hypothetical protein FLJ22557 Hs.106101 H00595 1146 FLJ20539:hypothetical protein FLJ20539 Hs.118552 R36152 1147 AA991624: 1148TRAP150: thyroid hormone receptor-associated protein, 150 kDa subunitHs.108319 W85832 1149 ESTs: Hs.221847 R91557 1150 TCFL1: transcriptionfactor-like 1 Hs.2430 AA443950 1151 ESTs,: Highly similar to oxytocinasesplice variant 1 [H. sapiens] Hs.203271 AA487918 1152 PLAB: prostatedifferentiation factor Hs.296638 AA450062 1153 RBM14: RNA binding motifprotein 14 Hs.11170 AA417283 1154 EGFL5: EGF-like-domain, multiple 5Hs.5599 W67981 1155 H2AFO: H2A histone family, member O Hs.795 AA0472601156 ESTs,: Weakly similar to A46661 leukotriene B4 omega-hydroxylase[H. sapiens] Hs.169001 N45556 1157 W78784: 1158 TOP3A: topoisomerase(DNA) III alpha Hs.91175 N21546 1159 W73732: Host cell factor-1 = VP16transactivator interacting protein 1160 CYP1B1: cytochrome P450,subfamily I (dioxin-inducible), polypeptide 1 (glaucoma 3, primaryinfantile) Hs.154654 AA448157 Cytochrome P450 IB1 (dioxin-inducible)1161 ESTs: Hs.135276 AI092102 1162 RHEB2: Ras homolog enriched in brain2 Hs.279903 AA482117 1163 ESTs,: Highly similar to EF-9 [M. musculus]Hs.8366 H94467 1164 POLA: polymerase (DNA directed), alpha Hs.267289AA707650 1165 KIAA1008: KIAA1008 protein Hs.323346 AA863115 1166 PIK3CD:phosphoinositide-3-kinase, catalytic, delta polypeptide Hs.162808AA281652 1167 T53625: 1168 **Homo sapiens mRNA; cDNA DKFZp434A1114 (fromclone DKFZp434A1114) Hs.326292 AA417274: 1169 ESTs: Hs.26744 H16988 1170FLJ13912: hypothetical protein FLJ13912 Hs.47125 W74133 1171 Homosapiens mRNA; cDNA DKFZp762B195 (from clone DKFZp762B195) Hs.284158AA625574: 1172 SSA2: Sjogren syndrome antigen A2 (60 kD,ribonucleoprotein autoantigen SS-A/Ro) Hs.554 AA010351 1173 BK1048E9.5:hypothetical protein bK1048E9.5 Hs.6657 N68512 1174 TOP1: topoisomerase(DNA) I Hs.317 AA232856 Topoisomerase I 1175 ESTs: Hs.15386 H18472 1176KPNB1: karyopherin (importin) beta 1 Hs.180446 AA121732 1177 MGC861:hypothetical protein MGC861 Hs.208912 N69694 1178 PMS2L8: **postmeioticsegregation increased 2-like 8 Hs.323954 T62577 1179 TSC22:**transforming growth factor beta-stimulated protein TSC-22 Hs.114360R16390 1180 C8ORF1: chromosome 8 open reading frame 1 Hs.40539 AA2788361181 ESTs: Hs.129165 AA989211 1182 DMTF: cyclin D binding Myb-liketranscription factor 1 Hs.5671 AA129860 1183 CDC7L1: CDC7 (cell divisioncycle 7, S. cerevisiae, homolog)-like 1 Hs.28853 N62245 Cdc7-relatedkinase 1184 LOC51700: cytochrome b5 reductase b5R.2 Hs.22142 AA4253161185 FLNA: filamin A, alpha (actin-binding protein-280) Hs.195464AA598978 1186 FLJ20257: hypothetical protein FLJ20257 Hs.178011 H786751187 Homo sapiens cDNA FLJ13604 fis, clone PLACE1010401 Hs.23193AA406599: 1188 ESTs: Hs.205227 R73480 1189 SCYB14: small induciblecytokine subfamily B (Cys-X-Cys), member 14 (BRAK) Hs.24395 AA9538421190 MAPK8IP2: **mitogen-activated protein kinase 8 interacting protein2 Hs.80545 AA418293 1191 ZNF42: zinc finger protein 42 (myeloid-specificretinoic acid-responsive) Hs.169832 AA932642 1192 ESTs: Hs.127054AA862450 1193 NUDT4: nudix (nucleoside diphosphate linked moiety X)-typemotif 4 Hs.92381 AA425630 1194 Homo sapiens cDNA FLJ10632 fis, cloneNT2RP2005637 Hs.202596 H82421: 1195 LOC51042: zinc finger proteinHs.102419 AA033532 1196 NUMA1: nuclear mitotic apparatus protein 1Hs.301512 AA679293 1197 ESTs,: Highly similar to A56429I-kappa-B-related protein [H. sapiens] Hs.144614 AA293771 1198 ESTs:Hs.127703 AA947258 1199 Homo sapiens cDNA FLJ14214 fis, cloneNT2RP3003576 Hs.321236 AA903913: 1200 NFKBIA: nuclear factor of kappalight polypeptide gene enhancer in B-cells inhibitor, alpha Hs.81328W55872 IkB alpha 1201 ESTs: Hs.120029 AA707598 1202 ESTs,: Moderatelysimilar to A Chain A, Human Glucosamine-6-Phosphate Deaminase IsomeraseAt 1.75 A [H. sapiens] Hs.21398 AA172012 1203 NFIA: nuclear factor I/AHs.173933 AI912047 1204 RECQL4: RecQ protein-like 4 Hs.31442 AA6204461205 **ESTs,: Weakly similar to ALU1_HUMAN ALU SUBFAMILY J SEQUENCECONTAMINATION WARNING ENTRY [H. sapiens] Hs.318894 R96212 1206 Homosapiens cDNA: FLJ21686 fis, clone COL09379 Hs.20787 R11371: 1207LOC57168: similar to aspartate beta hydroxylase (ASPH) Hs.184390 H172721208 ESTs: Hs.26096 R54109 1209 Homo sapiens OSBP-related protein 6mRNA, complete cds Hs.318775 AA680281: 1210 APACD: ATP binding proteinassociated with cell differentiation Hs.153884 N80741 1211 VIM:**vimentin Hs.297753 AI668662 1212 Homo sapiens cDNA FLJ13618 fis, clonePLACE1010925 Hs.17448 AA427980: 1213 NR3C1: nuclear receptor subfamily3, group C, member 1 Hs.75772 N30428 Glucocorticoid receptor 1214 Homosapiens cDNA: FLJ21814 fis, clone HEP01068 Hs.289008 R12808: 1215 BRD7:bromodomain-containing 7 Hs.279762 AA488428 1216 MAP3K8:**mitogen-activated protein kinase kinase kinase 8 Hs.248 W42450 1217ESTs: Hs.23213 H29336 1218 ESTs: Hs.122444 AA939019 1219 TUSP: tubbysuper-family protein Hs.102237 H78234 1220 KIAA1117: KIAA1117 proteinHs.278398 H01516 1221 Human: clone 137308 mRNA, partial cds Hs.322149H91303 1222 ESTs: Hs.130214 AA456631 1223 RAB3A: RAB3A, member RASoncogene family Hs.27744 H14230 1224 AA598795: Protein phosphatase 2(formerly 2A), regulatory subunit B (P 1225 H2BFC: H2B histone family,member C Hs.137594 AI340654 1226 CFLAR: CASP8 and FADD-like apoptosisregulator Hs.195175 N94588 1227 CD24: CD24 antigen (small cell lungcarcinoma cluster 4 antigen) Hs.286124 H59915 1228 EST: Hs.48532 N624021229 CCRK: cell cycle related kinase Hs.26322 H17616 1230 HECH:heterochromatin-like protein 1 Hs.278554 AI139106 1231 DKFZp547O146:hypothetical protein DKFZp547O146 Hs.91246 T80848 1232 ESTs: Hs.71574AA135328 1233 HLXB9: homeo box HB9 Hs.37035 AI459915 1234 AA600222: 1235SPINK5: serine protease inhibitor, Kazal type, 5 Hs.5476 W92134 1236RNUT1: RNA, U transporter 1 Hs.21577 AA447799 1237 Homo sapiens cDNA:FLJ23013 fis, clone LNG00740 Hs.13075 AA464543: 1238 KIAA0063: KIAA0063gene product Hs.3094 T82263 1239 DYRK2: dual-specificitytyrosine-(Y)-phosphorylation regulated kinase 2 Hs.173135 R63622 1240R94947: 1241 Homo sapiens cDNA FLJ14337 fis, clone PLACE4000494Hs.180187 AA004903: 1242 FLJ20624: hypothetical protein FLJ20624Hs.52256 AA431909 1243 ESTs: Hs.43838 R38261 1244 FLJ23053: hypotheticalprotein FLJ23053 Hs.94037 R25654 1245 MGC11266: hypothetical proteinMGC11266 Hs.293943 AA400456 1246 ESTs,: Moderately similar to ALU8_HUMANALU SUBFAMILY SX SEQUENCE CONTAMINATION WARNING ENTRY [H. sapiens]Hs.34174 AA126603 1247 PLAUR: plasminogen activator, urokinase receptorHs.179657 AA147962 1248 TSG101: tumor susceptibility gene 101 Hs.118910AA670215 1249 HCNGP: transcriptional regulator protein Hs.27299 AA4572321250 KIAA0978: KIAA0978 protein Hs.3686 AA857017 1251 ESTs: Hs.61708AA033867 1252 ESTs: Hs.120734 AA827482 1253 ESTs: Hs.5909 AA972654 1254CDH24: cadherin-like 24 Hs.155912 AI668564 1255 CCND1: cyclin D1 (PRAD1:parathyroid adenomatosis 1) Hs.82932 T77237 1256 ESTs: Hs.43148 AA2847751257 ESTs: Hs.222566 T50982 1258 ESTs: Hs.194125 N52822 1259 EST:Hs.154621 AI138644 1260 MAN1A2: mannosidase, alpha, class 1A, member 2Hs.239114 R22905 1261 MAN2A2: mannosidase, alpha, class 2A, member 2Hs.295605 AA454175 1262 Human DNA sequence from clone 967N21 onchromosome 20p12.3-13. Contains the CHGB gene for chromogranin B(secretogranin 1, SCG1), a pseudogene similar to part of KIAA0172, thegene for a novel protein Hs.88959 W94690 1263 ESTs,: Highly similar toCIKG_HUMAN VOLTAGE-GATED POTASSIUM CHANNEL PROTEIN KV3.4 [H. sapiens]Hs.106486 H11376 1264 Homo sapiens HT023 mRNA, complete cds Hs.237225AA169496: 1265 FLJ10339: **hypothetical protein FLJ10339 Hs.203963H72354 1266 N66278: 1267 ESTs: Hs.6195 AA454745 1268 KIAA1404: KIAA1404protein Hs.200317 W72798 1269 PMAIP1:phorbol-12-myristate-13-acetate-induced protein 1 Hs.96 AA458838 APR =immediate-early-response gene = ATL-derived PMA-responsive 1270 G3BP:Ras-GTPase-activating protein SH3-domain-binding protein Hs.220689AA598628 1271 Homo sapiens cDNA: FLJ22807 fis, clone KAIA2887 Hs.261734R26854: 1272 Homo sapiens, clone IMAGE: 3535294, mRNA, partial cdsHs.80449 T57359: 1273 CDC16: CDC16 (cell division cycle 16, S.cerevisiae, homolog) Hs.1592 AA410559 1274 FGA: **fibrinogen, A alphapolypeptide Hs.90765 AA026626 1275 ESTs: Hs.33446 N53560 1276 Homosapiens cDNA FLJ14175 fis, clone NT2RP2002979 Hs.288613 AA054704: 1277ESTs: Hs.44243 AA011390 1278 Homo sapiens mRNA full length insert cDNAclone EUROIMAGE 42408 Hs.284123 R61732: 1279 ESTs: Hs.53455 AA4541651280 FLJ11264: hypothetical protein FLJ11264 Hs.11260 AI219094 1281MBD4: methyl-CpG binding domain protein 4 Hs.35947 AA010492 1282FLJ11305: hypothetical protein FLJ11305 Hs.7049 N94612 1283 Homosapiens, Similar to CG5057 gene product, clone MGC: 5309, mRNA, completecds Hs.13885 AA460004: 1284 ARHB: ras homolog gene family, member BHs.204354 H88963 1285 ITPR3: inositol 1,4,5-triphosphate receptor, type3 Hs.77515 AA865667 1286 HMG20B: high-mobility group 20B Hs.32317AA775743 1287 ESTs: Hs.146276 AI214204 1288 PTPN9: protein tyrosinephosphatase, non-receptor type 9 Hs.147663 AA434420 1289 Homo sapiensclone FLB9213 PRO2474 mRNA, complete cds Hs.21321 AA486770: 1290 H21107:1291 HSPC157: HSPC157 protein Hs.279842 N20480 1292 Homo sapiens mRNA;cDNA DKFZp564O2363 (from clone DKFZp564O2363) Hs.321403 AA406332: 1293ESTs: Hs.150623 AA693532 1294 EST: Hs.188697 AA199733 1295 CLECSF2:C-type (calcium dependent, carbohydrate-recognition domain) lectin,superfamily member 2 (activation-induced) Hs.85201 H11732 AICL =activation- induced C-type lectin 1296 ITPR1: inositol1,4,5-triphosphate receptor, type 1 Hs.198443 AA035450 1297 CHML:choroideremia-like (Rab escort protein 2) Hs.170129 R91881 1298 CDC42:cell division cycle 42 (GTP-binding protein, 25 kD) Hs.146409 AA6686811299 FKBP5: **FK506-binding protein 5 Hs.7557 AA872767

All publications and patent applications mentioned in the specificationare indicative of the level of those skilled in the art to which thisdisclosure pertains. All publications and patent applications are hereinincorporated by reference to the same extent as if each individualpublication or patent application was specifically and individuallyindicated to be incorporated by reference. The mere mentioning of thepublications and patent applications does not necessarily constitute anadmission that they are prior art to the instant application.

Although the foregoing disclosure has been described in some detail byway of illustration and example for purposes of clarity ofunderstanding, it will be obvious that certain changes and modificationsmay be practiced within the scope of the appended claims.

What is claimed is:
 1. A method for treating prostate cancer in apatient in need thereof who has previously been treated for the prostatecancer, the method comprising: measuring, in a sample obtained from thepatient, expression levels of PCA3 and at least three genes of a panelof genes comprising ASF1B, ASPM, BIRC5, BUB1B, C18orf24, CDC2, CDC20,CDCA3, CDCA8, CDKN3, CENPF, CENPM, CEP55, DLGAP5, DTL, FOXM1, KIAA0101,KIF11, KIF20A, MCM10, NUSAP1, ORC6L, PBK, PLK1, PRC1, PTTG1, RAD51,RAD54L, RRM2, TK1 and TOP2A; providing a test expression score by (a)weighting the determined expression of PCA3 and each of the at leastthree genes, and (b) combining the weighted expression of PCA3 and eachof the at least three genes to provide the test expression score,wherein the at least three genes are weighted to contribute at least 25%to the test expression score; prognosing the patient as having anincreased likelihood of cancer recurrence or cancer-specific death afterthe previous treatment for the prostate cancer and before recurrence ofthe prostate cancer based on the test expression score exceeding areference expression score of a reference population with the samecancer; and administering treatment to the patient, the treatmentcomprising one or more of hormonal therapy, chemotherapy, radiationtherapy, and surgical removal of cancer tissue.
 2. The method of claim1, wherein said test genes further comprise one or more AR signalinggenes.
 3. The method of claim 1, wherein expression levels arenormalized to expression of housekeeping genes.
 4. The method of claim1, wherein the reference expression score is a test expression scoreobtained from a reference population of prostate cancer patients.
 5. Amethod for treating prostate cancer in a patient in need thereof who haspreviously been treated for the prostate cancer, the method comprising:measuring in a sample obtained from the patient expression levels ofPCA3 and at least three genes of a panel of genes comprising ASF1B,ASPM, BIRC5, BUB1B, C18orf24, CDC2, CDC20, CDCA3, CDCA8, CDKN3, CENPF,CENPM, CEP55, DLGAP5, DTL, FOXM1, KIAA0101, KIF11, KIF20A, MCM10,NUSAP1, ORC6L, PBK, PLK1, PRC1, PTTG1, RAD51, RAD54L, RRM2, TK1 andTOP2A; providing a test expression score by (a) weighting the determinedexpression of each of PCA3 and the at least three genes, and (b)combining the weighted expression of PCA3 and each of the at least threegenes to provide the test expression score, wherein PCA3 and the atleast three genes are weighted to contribute at least 25% to the testexpression score; prognosing the patient as having a decreasedlikelihood of cancer recurrence or cancer-specific death based on thetest expression score being lower than a reference expression score of areference population with the same cancer; administering to the patientactive surveillance for a period of time until symptoms develop or thereare signs that the cancer growth is accelerating; and administeringtreatment to the patient before recurrence of the prostate cancer, thetreatment comprising one or more of hormonal therapy, chemotherapy,radiation therapy, and surgical removal of cancer tissue.
 6. The methodof claim 5, wherein expression levels are normalized to expression ofhousekeeping genes.
 7. The method of claim 5, wherein the referenceexpression score is a test expression score obtained from a referencepopulation of prostate cancer patients.